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<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
<|fim_middle|>
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
<|fim_middle|>
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
<|fim_middle|>
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
<|fim_middle|>
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
<|fim_middle|>
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
<|fim_middle|>
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
<|fim_middle|>
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
<|fim_middle|>
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
<|fim_middle|>
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
<|fim_middle|>
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1)) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
<|fim_middle|>
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_cf, op_zf = args
return op_cf | op_zf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
<|fim_middle|>
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_cf, = args
return ~op_cf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
<|fim_middle|>
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_nf, op_of = args
return op_nf ^ op_of |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
<|fim_middle|>
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of)) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
<|fim_middle|>
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
<|fim_middle|>
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_nf, op_of = args
return ~(op_nf ^ op_of) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
<|fim_middle|>
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_cf, op_zf = args
return ~(op_cf | op_zf) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
<|fim_middle|>
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_cf, = args
return op_cf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
<|fim_middle|>
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_nf, = args
return op_nf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
<|fim_middle|>
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_zf, = args
return op_zf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
<|fim_middle|>
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | op_zf, = args
return ~op_zf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
<|fim_middle|>
return expr
<｜fim▁end｜> | op_nf, = args
return ~op_nf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def <|fim_middle|>(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def simp_flags(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | simp_ext |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size:
return arg
return ExprCompose(arg, ExprInt(0, expr.size - arg.size))
if expr.op.startswith("signExt_"):
arg = expr.args[0]
add_size = expr.size - arg.size
new_expr = ExprCompose(
arg,
ExprCond(
arg.msb(),
ExprInt(size2mask(add_size), add_size),
ExprInt(0, add_size)
)
)
return new_expr
return expr
def <|fim_middle|>(_, expr):
args = expr.args
if expr.is_op("FLAG_EQ"):
return ExprCond(args[0], ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_EQ_AND"):
op1, op2 = args
return ExprCond(op1 & op2, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("FLAG_SIGN_SUB"):
return (args[0] - args[1]).msb()
elif expr.is_op("FLAG_EQ_CMP"):
return ExprCond(
args[0] - args[1],
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADD_CF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_CF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADD_OF"):
op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUB_OF"):
op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_EQ_ADDWC"):
op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
)
elif expr.is_op("FLAG_ADDWC_OF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_OF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_ADDWC_CF"):
op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb()
elif expr.is_op("FLAG_SUBWC_CF"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb()
elif expr.is_op("FLAG_SIGN_ADDWC"):
op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb()
elif expr.is_op("FLAG_SIGN_SUBWC"):
op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb()
elif expr.is_op("FLAG_EQ_SUBWC"):
op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1))
elif expr.is_op("CC_U<="):
op_cf, op_zf = args
return op_cf | op_zf
elif expr.is_op("CC_U>="):
op_cf, = args
return ~op_cf
elif expr.is_op("CC_S<"):
op_nf, op_of = args
return op_nf ^ op_of
elif expr.is_op("CC_S>"):
op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of))
elif expr.is_op("CC_S<="):
op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of)
elif expr.is_op("CC_S>="):
op_nf, op_of = args
return ~(op_nf ^ op_of)
elif expr.is_op("CC_U>"):
op_cf, op_zf = args
return ~(op_cf | op_zf)
elif expr.is_op("CC_U<"):
op_cf, = args
return op_cf
elif expr.is_op("CC_NEG"):
op_nf, = args
return op_nf
elif expr.is_op("CC_EQ"):
op_zf, = args
return op_zf
elif expr.is_op("CC_NE"):
op_zf, = args
return ~op_zf
elif expr.is_op("CC_POS"):
op_nf, = args
return ~op_nf
return expr
<｜fim▁end｜> | simp_flags |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,<｜fim▁hole｜> help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()<｜fim▁end｜> | |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
<|fim_middle|>
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | return 0 |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
<|fim_middle|>
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | return None |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
<|fim_middle|>
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | break |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
<|fim_middle|>
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | first_time_stamp = event.timestamp |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
<|fim_middle|>
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name)) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
<|fim_middle|>
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name)) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
<|fim_middle|>
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name)) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
<|fim_middle|>
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name)) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
<|fim_middle|>
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | print "No dump file to parse is set.\n"
parser.print_help()
exit() |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
<|fim_middle|>
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit() |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
<|fim_middle|>
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | f, mp_plot = plt.subplots()
plots.append(mp_plot) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
<|fim_middle|>
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist()) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
<|fim_middle|>
<｜fim▁end｜> | main() |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def <|fim_middle|>(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | GetNextMessageSize |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def <|fim_middle|>(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | GetNextMessageFromFile |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def <|fim_middle|>():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | InitMetrics |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def <|fim_middle|>():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | InitDecisions |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def <|fim_middle|>(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | ParseAnaDump |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def <|fim_middle|>():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | main |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
<|fim_middle|>
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0] |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
<|fim_middle|>
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
<|fim_middle|>
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
<|fim_middle|>
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
<|fim_middle|>
def main():
parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show()
if __name__ == "__main__":
main()
<｜fim▁end｜> | with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual property rights grant can be found
# in the file PATENTS. All contributing project authors may
# be found in the AUTHORS file in the root of the source tree.
# To run this script please copy "out/<build_name>//pyproto/webrtc/modules/
# audio_coding/audio_network_adaptor/debug_dump_pb2.py" to this folder.
# The you can run this script with:
# "python parse_ana_dump.py -m uplink_bandwidth_bps -f dump_file.dat"
# You can add as may metrics or decisions to the plot as you like.
# form more information call:
# "python parse_ana_dump.py --help"
import struct
from optparse import OptionParser
import matplotlib.pyplot as plt
import debug_dump_pb2
def GetNextMessageSize(file_to_parse):
data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0]
def GetNextMessageFromFile(file_to_parse):
message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event
def InitMetrics():
metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics
def InitDecisions():
decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions
def ParseAnaDump(dump_file_to_parse):
with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.timestamp
if event.type == debug_dump_pb2.Event.ENCODER_RUNTIME_CONFIG:
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name))
if event.type == debug_dump_pb2.Event.NETWORK_METRICS:
for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name))
return (metrics, decisions)
def main():
<|fim_middle|>
if __name__ == "__main__":
main()
<｜fim▁end｜> | parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')
parser.add_option(
'-d',
'--decision_plot',
default=[],
type=str,
help='decision key (name of the decision) to plot',
dest='decision_keys',
action='append')
options = parser.parse_args()[0]
if options.dump_file_to_parse == None:
print "No dump file to parse is set.\n"
parser.print_help()
exit()
(metrics, decisions) = ParseAnaDump(options.dump_file_to_parse)
metric_keys = options.metric_keys
decision_keys = options.decision_keys
plot_count = len(metric_keys) + len(decision_keys)
if plot_count == 0:
print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit()
plots = []
if plot_count == 1:
f, mp_plot = plt.subplots()
plots.append(mp_plot)
else:
f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist())
for key in metric_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (metric)")
plot.plot(metrics[key]['time'], metrics[key]['value'])
for key in decision_keys:
plot = plots.pop()
plot.grid(True)
plot.set_title(key + " (decision)")
plot.plot(decisions[key]['time'], decisions[key]['value'])
f.subplots_adjust(hspace=0.3)
plt.show() |
<|file_name|>__init__.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2021, DjaoDjin Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation<｜fim▁hole｜># AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
__version__ = '0.6.4-dev'<｜fim▁end｜> | # and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:<｜fim▁hole｜> self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)<｜fim▁end｜> | new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
<|fim_middle|>
<｜fim▁end｜> | """docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
<|fim_middle|>
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | '''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
<|fim_middle|>
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | '''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper()) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
<|fim_middle|>
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | '''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
<|fim_middle|>
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | '''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq))) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
<|fim_middle|>
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | '''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined"; |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
<|fim_middle|>
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain]) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
<|fim_middle|>
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain]) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
<|fim_middle|>
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | """Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
<|fim_middle|>
<｜fim▁end｜> | print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
<|fim_middle|>
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined"; |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
<|fim_middle|>
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined"; |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
<|fim_middle|>
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
<|fim_middle|>
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | new_viruses.append(v) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
<|fim_middle|>
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
<|fim_middle|>
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | print "\t\tresidual:", r, "\nremoved ",v.strain |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def <|fim_middle|>(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | __init__ |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def <|fim_middle|>(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | remove_insertions |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def <|fim_middle|>(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | clean_gaps |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def <|fim_middle|>(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | clean_ambiguous |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def <|fim_middle|>(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | unique_date |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def <|fim_middle|>(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | times_from_outgroup |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def <|fim_middle|>(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | distance_from_outgroup |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def <|fim_middle|>(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def clean_generic(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | clean_distances |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import stats
import numpy as np
class virus_clean(object):
"""docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper())
def clean_gaps(self):
'''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses)
def clean_ambiguous(self):
'''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq)))
def unique_date(self):
'''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined";
for ii, v in enumerate(self.viruses):
if hasattr(v, 'date'):
try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined";
def times_from_outgroup(self):
outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain])
def distance_from_outgroup(self):
from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])
def clean_distances(self):
"""Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - stats.scoreatpercentile(residuals,25)
if self.verbose:
print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd)
new_viruses = []
for (v,r) in izip(self.viruses,residuals):
# filter viruses more than n_std standard devitations up or down
if np.abs(r)<self.n_iqd * r_iqd or v.id == self.outgroup["strain"]:
new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain
self.viruses = MultipleSeqAlignment(new_viruses)
def <|fim_middle|>(self):
print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses)
<｜fim▁end｜> | clean_generic |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
pass
class ContactsUser(SimpleContactsUser):
pass
<｜fim▁hole｜><｜fim▁end｜> | class ContactsStaff(ContactsUser):
pass |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
<|fim_middle|>
class ContactsUser(SimpleContactsUser):
pass
class ContactsStaff(ContactsUser):
pass
<｜fim▁end｜> | pass |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
pass
class ContactsUser(SimpleContactsUser):
<|fim_middle|>
class ContactsStaff(ContactsUser):
pass
<｜fim▁end｜> | pass |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
pass
class ContactsUser(SimpleContactsUser):
pass
class ContactsStaff(ContactsUser):
<|fim_middle|>
<｜fim▁end｜> | pass |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):<｜fim▁hole｜> Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg<｜fim▁end｜> | """Constructeur du paramètre""" |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"<|fim_middle|>
<｜fim▁end｜> | ""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"<|fim_middle|>
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | ""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""<|fim_middle|>
ef interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
d |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Inte<|fim_middle|>
<｜fim▁end｜> | rprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnag <|fim_middle|>
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | e << "|err|Ce chemin n'existe pas.|ff|"
return
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n <|fim_middle|>
lse:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | Aucune"
e |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, <|fim_middle|>
personnage << msg
<｜fim▁end｜> | direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " ( <|fim_middle|>
personnage << msg
<｜fim▁end｜> | retour " + chemin.salles_retour[salle] + ")"
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def _<|fim_middle|>self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | _init__( |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajo<|fim_middle|>lf):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpreter(self, personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | uter(se |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Fichier contenant le paramètre 'voir' de la commande 'chemin'."""
from primaires.format.fonctions import oui_ou_non
from primaires.interpreteur.masque.parametre import Parametre
from primaires.pnj.chemin import FLAGS
class PrmVoir(Parametre):
"""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs, ses salles et sorties...)."
def ajouter(self):
"""Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
def interpr<|fim_middle|>personnage, dic_masques):
"""Interprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\n Flags :"
for nom_flag in FLAGS.keys():
msg += "\n {}".format(nom_flag.capitalize())
msg += " : " + oui_ou_non(chemin.a_flag(nom_flag))
msg += "\n Salles du chemin :"
if len(chemin.salles) == 0:
msg += "\n Aucune"
else:
for salle, direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_retour[salle] + ")"
personnage << msg
<｜fim▁end｜> | eter(self, |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python<｜fim▁hole｜># -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1)
def now(self):
"""Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60)
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date)
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now()<｜fim▁end｜> | |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
<|fim_middle|>
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date)
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now()
<｜fim▁end｜> | """Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1)
def now(self):
"""Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60) |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
<|fim_middle|>
def now(self):
"""Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60)
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date)
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now()
<｜fim▁end｜> | """Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1) |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1)
def now(self):
<|fim_middle|>
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date)
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now()
<｜fim▁end｜> | """Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60) |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1)
def now(self):
"""Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60)
if __name__ == '__main__':
# options
<|fim_middle|>
<｜fim▁end｜> | startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date)
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now() |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1)
def now(self):
"""Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60)
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
<|fim_middle|>
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now()
<｜fim▁end｜> | year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date) |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def <|fim_middle|>(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - datetime.timedelta(days=1)
def now(self):
"""Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
(curtime.seconds / 60) / 60,
(curtime.seconds / 60) % 60,
curtime.seconds % 60)
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timedelta(days=random.randint(0, daycount))
args = sys.argv
if len(args) == 4:
year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date)
print "birthdate:", birthdate.date()
mylife = DayLife(birthdate, life)
print "finaldate:", mylife.finaldate.date()
print "today:", mylife.now()
<｜fim▁end｜> | __init__ |
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