def build_score_dict(reads_dict, combined_dict, number_of_haplotypes, min_HF):
""" Returns a dicitonary lists read_IDs and gives their score. The scoring
algorithm scores each read according to the number of differet haplotypes
that the reference panel supports at the chromosomal region that overlaps
with the read. Only bialleic SNP with a minor allele frequeancy above
0.01 are considered for the calculation, since they are unlikely to affect
the score. In addition, only haplotypes with a frequnecy between min_HF
and 1-min_HF add to the score of a read. """
N = number_of_haplotypes
b = (1 << number_of_haplotypes
) - 1 #### equivalent to int('1'*number_of_haplotypes,2)
score_dict = dict()
for read_id in reads_dict:
haplotypes = (
(combined_dict[pos][-1], combined_dict[pos][-1] ^ b)
for pos, base in reads_dict[read_id]
if 0.01 <= popcount(combined_dict[pos][-1]) / N <= 0.99
) #Include only biallelic SNPs with MAF of at least 0.01. Also, ^b flips all bits of the binary number, hap_tab[ind] using bitwise xor operator.
score_dict[read_id] = sum(
min_HF <= popcount(reduce(and_, hap)) / N <= (1 - min_HF)
for hap in product(*haplotypes) if len(hap) != 0)
return score_dict
def checkGroup(self, state=None, player=None):
if state is None:
st = self.state
else:
st = state
if player is None:
p = self.currentPlayer
else:
p = player
areGrouped = True
if gmpy2.popcount(st[p]) == 1:
areGrouped = True
else:
unvisited = st[p]
checklist = 2**gmpy2.bit_scan1(unvisited)
unvisited ^= checklist
while gmpy2.popcount(checklist) > 0:
current = gmpy2.bit_scan1(checklist)
checklist ^= 2**current
currentNeighbours = self.neighbourhood[current] & unvisited
if currentNeighbours:
unvisited ^= currentNeighbours
checklist |= currentNeighbours
if gmpy2.popcount(unvisited) > 0:
areGrouped = False
return areGrouped
def joint_frequencies_combo(self, *alleles, normalize):
""" Based on the reference panel, it calculates joint frequencies of
observed alleles. The function arguments are alleles, that is,
tuples of position and base, e.g., (100,'T'), (123, 'A') and
(386, 'C'). Each allele is enumerated according to the order it
was received by the function. The function returns a dictionary that
lists all the possible subgroups of the given alleles. Each key in
the dictionary is a tuple of intergers that are lexicographically
sorted. Moreover, each integer within the keys corresponds to an
enumerated allele. For each subgroup of alleles the dictionary
gives the joint frequencies in a given population. The function
arguments can also include haplotypes, that is, tuples of alleles;
Haplotypes are treated in the same manner as alleles. """
hap = self.intrenal_hap_dict(*alleles)
result = {c: popcount(A) for c,A in hap.items() }
for C in combinations(hap, 2):
result[C[0]|C[1]] = popcount(hap[C[0]]&hap[C[1]])
for C in combinations(hap, 3):
result[C[0]|C[1]|C[2]] = popcount(hap[C[0]]&hap[C[1]]&hap[C[2]])
for r in range(4,len(alleles)):
for C in combinations(hap, r):
result[sum(C)] = popcount(reduce(and_,itemgetter(*C)(hap)))
if len(alleles)>=4:
result[sum(hap.keys())] = popcount(reduce(and_,hap.values()))
if normalize:
result = {k: v/self.total_number_of_haplotypes_in_reference_panel for k,v in result.items()}
return result
def get_ground_state(self,verbose=False):
'''
:return: The ground state of the Hamiltonian
'''
e,v = scipy.linalg.eigh(self.H)
if(verbose):
print("energies : ")
print(np.around(e,2))
index=np.argsort(e)
n_degenerate = 1
continuer = True
gs=[v[:,0]]
#we also want to fix the number of electrons (avoid degeneracy with different numbers of electrons
index_el = np.where(np.abs(v[:,0])>0.0001)[0]
n_el = gmpy2.popcount(int(index_el[0]))
while(continuer):
if(np.abs(e[index[n_degenerate]]-e[index[0]])<0.00000001):
index_bis = np.where(np.abs(v[:, index[n_degenerate]]) > 0.00001)[0]
n_el_bis=0
for runner in index_bis:
n_el_bis += gmpy2.popcount(int(runner))
n_el_bis/=len(index_bis)
if np.abs(n_el_bis-n_el)<0.001:
gs.append(v[:,index[n_degenerate]])
n_degenerate+=1
else:
continuer=False
return gs
def _add_subgroup2list(self, subgroup2add):
self.bitset_covered = self.bitset_covered | subgroup2add.bitarray
self.support_covered = popcount(self.bitset_covered)
self.bitset_uncovered = self.bitset_uncovered & ~subgroup2add.bitarray
self.support_uncovered = popcount(self.bitset_uncovered)
self.bitset_rules.append(subgroup2add.bitarray)
self.subgroups.append(deepcopy(subgroup2add))
return self
def is_insufficient_material(self):
if popcount(self.occupancy) == 2:
return True
elif popcount(self.occupancy) == 3:
if (self.piece_bb[W_KNIGHT] or self.piece_bb[B_KNIGHT]
or self.piece_bb[W_BISHOP] or self.piece_bb[B_BISHOP]):
return True
return False
def bit_solver(shift: int, player: Bitmap, not_player: Bitmap):
"""
Calculates the heuristic score for a particular orientation of pieces
(i.e. vertically aligned, horizontally aligned, right diagonal or left
diagonal). Each direction has a unique shift value in the bitmap.
:param shift: bit shift of the current direction being calculated
:param player: bitmap representing positions of the current player
:param not_player: bitmap representing positions of the other player
:return: the score associated with this particular direction
"""
# Initialize the score and point values
score = 0
pt2 = 1
pt3 = 10
s1_right = (player >> shift)
s2_right = player >> (2 * shift)
s3_right = player >> (3 * shift)
s1_left = (player << shift)
s2_left = player << (2 * shift)
s3_left = player << (3 * shift)
s1_right_n1 = s1_right & player
s1_left_n1 = s1_left & player
# Check for 3 in 4
# XXX-
score += pt3 * popcount(((s1_left_n1 & s2_left) << shift) & not_player)
# -XXX
score += pt3 * popcount(((s1_right_n1 & s2_right) >> shift) & not_player)
# XX-X
score += pt3 * popcount((s1_right_n1 & s3_right) << (2 * shift)
& not_player)
# X-XX
score += pt3 * popcount((s1_left_n1 & s3_left) >> (2 * shift) & not_player)
# Check for 2 in 4
# XX--
score += pt2 * popcount(s1_left_n1 << shift
& (not_player & (not_player >> shift)))
# --XX
score += pt2 * popcount(s1_right_n1 >> shift
& (not_player & (not_player << shift)))
# X-X-
score += pt2 * popcount((player & s2_left) << shift
& (not_player & (not_player << (2 * shift))))
# -X-X
score += pt2 * popcount((player & s2_right) >> shift
& (not_player & (not_player >> (2 * shift))))
# X--X
score += pt2 * popcount((player & s3_right) << shift
& (not_player & (not_player >> shift)))
# -XX-
score += pt2 * popcount(s1_right_n1 >> shift
& (not_player & (not_player >> (3 * shift))))
return score
def bit_solver(shift: int, player: Bitmap, not_player: Bitmap):
"""
"""
# Initialize the score and point values
score = 0
pt2 = 1
pt3 = 10
# win_pts = 100
s1_right = (player >> shift)
s2_right = player >> (2 * shift)
s3_right = player >> (3 * shift)
s1_left = (player << shift)
s2_left = player << (2 * shift)
s3_left = player << (3 * shift)
s1_right_n1 = s1_right & player
s1_left_n1 = s1_left & player
# Check for wins
# score += win_pts * popcount(s1_left_n1 & (s1_left_n1 >> (2 * shift)))
# Check for 3 in 4
# XXX-
score += pt3 * popcount(((s1_left_n1 & s2_left) << shift)
& not_player)
# -XXX
score += pt3 * popcount(((s1_right_n1 & s2_right) >> shift)
& not_player)
# XX-X
score += pt3 * popcount((s1_right_n1 & s3_right) << (2 * shift)
& not_player)
# X-XX
score += pt3 * popcount((s1_left_n1 & s3_left) >> (2 * shift)
& not_player)
# Check for 2 in 4
# XX--
score += pt2 * popcount(s1_left_n1 << shift
& (not_player & (not_player >> shift)))
# --XX
score += pt2 * popcount(s1_right_n1 >> shift
& (not_player & (not_player << shift)))
# X-X-
score += pt2 * popcount((player & s2_left) << shift
& (not_player & (not_player << (2 * shift))))
# -X-X
score += pt2 * popcount((player & s2_right) >> shift
& (not_player & (not_player >> (2 * shift))))
# X--X
score += pt2 * popcount((player & s3_right) << shift
& (not_player & (not_player >> shift)))
# -XX-
score += pt2 * popcount(s1_right_n1 >> shift
& (not_player & (not_player >> (3 * shift))))
return score
def evaluate_pawns(self, position):
pawn_table_index = position.pawn_key & 0xFFFF
pawn_entry = self.pawn_table[pawn_table_index]
if pawn_entry and pawn_entry.key == position.pawn_key:
return pawn_entry.score_mg, pawn_entry.score_eg
king_sqr = None
score_mg = [0, 0]
score_eg = [0, 0]
for colour in COLOURS:
player_pawns = position.piece_bb[(colour << 3) | PAWN]
enemy_pawns = position.piece_bb[((colour ^ 1) << 3) | PAWN]
enemy_pawn_attacks = (pawn_shift[colour ^ 1](enemy_pawns, NORTHEAST)
| pawn_shift[colour ^ 1](enemy_pawns, NORTHWEST))
for sq in gen_bitboard_indices(player_pawns):
pawn_bb = 1 << sq
adjacent_squares = adjacent_files[sq] & rank_of[sq]
adjacent_pawns = adjacent_files[sq] & player_pawns
aligned = True if adjacent_squares & player_pawns else False
defenders = adjacent_pawns & pawn_shift[colour ^ 1](rank_of[sq], NORTH)
opposed = True if forward_fill[colour](pawn_bb) & enemy_pawns else False
# Doubled pawn
if (player_pawns & pawn_shift[colour ^ 1](pawn_bb, NORTH)) and not defenders:
score_mg[colour] -= DOUBLED[MIDGAME]
score_eg[colour] -= DOUBLED[ENDGAME]
# Connected pawn
if aligned or defenders:
score_mg[colour] += connected_bonus[opposed][aligned][popcount(defenders)][(sq >> 3) ^ (colour * 7)][MIDGAME]
score_eg[colour] += connected_bonus[opposed][aligned][popcount(defenders)][(sq >> 3) ^ (colour * 7)][ENDGAME]
# Isolated pawn
elif not adjacent_pawns:
score_mg[colour] -= ISOLATED[MIDGAME]
score_eg[colour] -= ISOLATED[ENDGAME]
# Backward pawn
elif (pawn_shift[colour](pawn_bb, NORTH) & (enemy_pawns | enemy_pawn_attacks)
and not forward_fill[colour ^ 1](adjacent_squares) & player_pawns):
score_mg[colour] -= BACKWARD[MIDGAME]
score_eg[colour] -= BACKWARD[ENDGAME]
score_mg = score_mg[WHITE] - score_mg[BLACK]
score_eg = score_eg[WHITE] - score_eg[BLACK]
self.pawn_table[pawn_table_index] = PawnEntry(position.pawn_key, score_mg, score_eg)
return score_mg, score_eg
def test_delete(self):
for flags in xrange(16):
pn = MemoryPatriciaDict()
pn.update((k,v) for k,v in six.iteritems(SCENARIOS[flags]) if k != 'hash_')
for idx,scenario in enumerate(SCENARIOS):
items = [(k,v) for k,v in six.iteritems(scenario) if k != 'hash_']
pn2 = MemoryPatriciaDict()
pn2.update(pn)
self.assertEqual(pn2.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn2.size, gmpy2.popcount(flags))
self.assertEqual(pn2.length, gmpy2.popcount(flags))
pn3 = MemoryPatriciaDict()
pn3.update(pn)
self.assertEqual(pn3.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags))
self.assertEqual(pn3.length, gmpy2.popcount(flags))
for (k,v) in items:
if k in SCENARIOS[flags]:
pn2.delete([k])
pn3.delete(iter([k]))
else:
with self.assertRaises(KeyError):
pn2.delete([k])
with self.assertRaises(KeyError):
pn3.delete(iter([k]))
self.assertEqual(pn2.hash, SCENARIOS[flags & ~idx]['hash_'])
self.assertEqual(pn2.size, gmpy2.popcount(flags & ~idx))
self.assertEqual(pn2.length, gmpy2.popcount(flags & ~idx))
self.assertEqual(pn3.hash, SCENARIOS[flags & ~idx]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags & ~idx))
self.assertEqual(pn3.length, gmpy2.popcount(flags & ~idx))
def test_delete(self):
for flags in range(16):
pn = MemoryPatriciaAuthTree()
pn.update((k,v) for k,v in six.iteritems(SCENARIOS[flags]) if k != 'hash_')
for idx,scenario in enumerate(SCENARIOS):
items = [(k,v) for k,v in six.iteritems(scenario) if k != 'hash_']
pn2 = MemoryPatriciaAuthTree()
pn2.update(pn)
self.assertEqual(pn2.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn2.size, gmpy2.popcount(flags))
self.assertEqual(pn2.length, gmpy2.popcount(flags))
pn3 = MemoryPatriciaAuthTree()
pn3.update(pn)
self.assertEqual(pn3.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags))
self.assertEqual(pn3.length, gmpy2.popcount(flags))
for (k,v) in items:
if k in SCENARIOS[flags]:
pn2.delete([k])
pn3.delete(iter([k]))
else:
with self.assertRaises(KeyError):
pn2.delete([k])
with self.assertRaises(KeyError):
pn3.delete(iter([k]))
self.assertEqual(pn2.hash, SCENARIOS[flags & ~idx]['hash_'])
self.assertEqual(pn2.size, gmpy2.popcount(flags & ~idx))
self.assertEqual(pn2.length, gmpy2.popcount(flags & ~idx))
self.assertEqual(pn3.hash, SCENARIOS[flags & ~idx]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags & ~idx))
self.assertEqual(pn3.length, gmpy2.popcount(flags & ~idx))
def cvc_kifu(self, count):
ban = Ban().init_ban()
color = 0
pb = ban.bb
ob = ban.wb
kifulist_ = []
while True:
if not Play().legal_board(pb, ob):
mv = 64
vb = (ban.bb | ban.wb) ^ 0xffffffffffffffff
kifu = np.array([ban.bb, ban.wb, vb, color, mv],
dtype='uint64')
kifulist_.append(kifu)
color ^= 1
pb, ob = ob, pb
if not Play().legal_board(pb, ob):
mv = 64
vb = (ban.bb | ban.wb) ^ 0xffffffffffffffff
kifu = np.array([ban.bb, ban.wb, vb, color, mv],
dtype='uint64')
kifulist_.append(kifu)
break
mp = Move().rand_move(pb, ob)
# move_positionをmove_valueに変換
mv = 63 - popcount(mp - 1)
vb = (ban.bb | ban.wb) ^ 0xffffffffffffffff # void_board
kifu = np.array([ban.bb, ban.wb, vb, color, mv], dtype='uint64')
kifulist_.append(kifu)
# player_board, opponent_board更新
pb, ob = Play().put_turn(pb, ob, mp)
# board更新
ban = Play().set_board(pb, ob, color)
# 手番とplayer_board, opponent_board入れ替え
color ^= 1
pb, ob = ob, pb
kifulist = np.array(kifulist_, dtype='uint64')
bs = popcount(ban.bb)
ws = popcount(ban.wb)
row_num = kifulist.shape[0]
if bs >= ws:
r = np.zeros((row_num, 1))
kifulist = np.append(kifulist, r, axis=1)
elif bs < ws:
r = np.ones((row_num, 1))
kifulist = np.append(kifulist, r, axis=1)
np.save(
'./kifu/{0}-{1}'.format(
datetime.now().strftime('%y_%m_%d_%H_%M_%S_%f'), count),
kifulist)
def refine_subgroup(rulelist,data,candidate2refine,beam,subgroup2add):
""" Expands a subgroup by adding an item from all other variables not included in the subgroup.
"""
bitarray_candidate = reduce((lambda x, y: x & y), (item.bitarray for item in candidate2refine)) \
if candidate2refine != [] else bit_mask(data.number_instances)
#TODO: move this computation depending if it is a rule list or a rule set
bitarray_candidate = bitarray_candidate & rulelist.bitset_uncovered
variable_list = [item.parent_variable for item in candidate2refine]
for attribute in filter(lambda x: x.name not in variable_list, data.attributes):
#for item in attribute.generate_items(candidate2refine):
for item in attribute.items:
bitarray_newcandidate = bitarray_candidate & item.bitarray
usage = popcount(bitarray_newcandidate)
if usage >= rulelist.min_support:
new_subgroup_statistics, new_default_rule_statistics = \
compute_statistics_newrules(rulelist, data,bitarray_newcandidate)
new_candidate = candidate2refine + [item]
score, gain_data, gain_model = compute_delta_score(rulelist, new_candidate, new_subgroup_statistics, new_default_rule_statistics)
else:
score = np.NINF
if score > subgroup2add.score:
subgroup2add.update(new_candidate, new_subgroup_statistics, gain_data, gain_model, score)
if score > beam.min_score and set([item.description for item in new_candidate]) not in beam.set_patterns:
beam.replace(new_candidate, score, usage)
#print("Subgroup: {} ; score : {}".format([pat.parent_variable for pat in new_candidate],score))
return beam, subgroup2add
def calc_ber(src, dst, m):
"""Calculate bit error rate (BER)
Parameters
----------
src: array_like
dst: array_like, whose shape should be same to `src`.
m: modulation level, such as 2, 4, 8, ...
This is required to calculate number of bits for each symbol.
Returns
-------
SER
"""
if src.shape != dst.shape:
raise ValueError("Shape consistency error.")
if (dst < 0).any():
raise ValueError("Negative value(s) are found.")
if (src < 0).any():
raise ValueError("Negative value(s) are found.")
x = src ^ dst
# pylint: disable=no-member
if __gmpy2:
f = np.vectorize(lambda i: gmpy2.popcount(int(i)))
else:
f = np.vectorize(lambda i: bin(i).count('1'))
x = x[np.where(x != 0)]
c = np.sum(f(x)) if np.size(x == 0) else 0
return c / (np.log2(m) * np.size(src))
def generate_full_board(player, empty_spaces=0):
# Generate an empty board
arr_board = cm.initialize_game_state()
# Convert board to bitmap
bit_board, bit_mask = cm.board_to_bitmap(arr_board, player)
# Calculate the board shape
bd_shp = arr_board.shape
# While the board is not full, continue placing pieces
while popcount(bit_mask) != bd_shp[0] * bd_shp[1] - empty_spaces:
# Select a random move in a column that is not full
move = -1
while not (0 <= move < bd_shp[1]):
move = np.random.choice(bd_shp[1])
try:
move = cm.PlayerAction(move)
cm.top_row(arr_board, move)
except IndexError:
move = -1
# Apply the move to both boards
cm.apply_action(arr_board, move, player)
bit_board, bit_mask = cm.apply_action_cp(bit_board, bit_mask, move,
bd_shp)
# Switch to the next player
player = cm.BoardPiece(player % 2 + 1)
return arr_board, bit_board, bit_mask, player
def gnubg_id_str_to_board_id(config, pos_id_str):
"""Convert a Base64 endcoded position ID from gnubg to a board ID.
See
https://www.gnu.org/software/gnubg/manual/html_node/A-technical-description-of-the-Position-ID.html
for a description of their position id encoding.
Args:
config: board.GameConfiguration
pos_id_str: Base64 encoded position ID from gnubg
Returns:
int
"""
pos_id = int.from_bytes(base64.b64decode(pos_id_str + '=='),
byteorder='little')
# pos_id is just like our encoding except they don't explictly
# have the bits for markers off the board. We'll just count how many
# markers there are and add those 1s in.
missing_markers = config.num_markers - gmpy2.popcount(pos_id)
modified_pos_id = ((pos_id <<
(missing_markers + 1)) | ~(~0 << missing_markers))
return modified_pos_id
def evaluate_mobility(self, position, mobility_bb):
mobility_area = [0, 0]
mobility_score_mg = [0, 0]
mobility_score_eg = [0, 0]
mobility_area[WHITE] = self.get_mobility_area(position, WHITE)
mobility_area[BLACK] = self.get_mobility_area(position, BLACK)
for sq in gen_bitboard_indices(mobility_bb):
piece = position.squares[sq]
piece_type = piece & 7
piece_colour = piece >> 3
if piece_type == KNIGHT:
moves = pseudo_attacks[KNIGHT][sq]
elif piece_type == BISHOP:
moves = batk_table[sq][(position.occupancy ^ position.piece_bb[(piece_colour << 3) | QUEEN]) & bishop_masks[sq]]
elif piece_type == ROOK:
moves = ratk_table[sq][(position.occupancy ^ position.piece_bb[(piece_colour << 3) | ROOK]
^ position.piece_bb[(piece_colour << 3) | QUEEN]) & rook_masks[sq]]
elif piece_type == QUEEN:
moves = ratk_table[sq][position.occupancy & rook_masks[sq]] | batk_table[sq][position.occupancy & bishop_masks[sq]]
moves &= mobility_area[piece_colour]
move_count = popcount(moves)
mobility_score_mg[piece_colour] += mobility[piece_type][move_count][MIDGAME]
mobility_score_eg[piece_colour] += mobility[piece_type][move_count][ENDGAME]
score_mg = mobility_score_mg[WHITE] - mobility_score_mg[BLACK]
score_eg = mobility_score_eg[WHITE] - mobility_score_eg[BLACK]
return score_mg, score_eg
def bitset(self,tid_bitsets):
if self.pattern:
tid_pattern = tid_bitsets[self.pattern[0]]
for item in self.pattern:
tid_pattern &= tid_bitsets[item]
self.bitset = tid_pattern
self.support_total = popcount(self.bitset)
return self
def replace_stats(self, data, index_bitarray):
self.usage = self.update_usage(index_bitarray)
for varname, bit_arrays_class in data.targets_info.bit_arrays_var_class.items(
):
for category in data.targets_info.categories[varname]:
self.usage_per_class[varname][category] = popcount(
index_bitarray & bit_arrays_class[category])
return self
def evaluate(self, position):
knights = position.piece_bb[W_KNIGHT] | position.piece_bb[B_KNIGHT]
bishops = position.piece_bb[W_BISHOP] | position.piece_bb[B_BISHOP]
rooks = position.piece_bb[W_ROOK] | position.piece_bb[B_ROOK]
queens = position.piece_bb[W_QUEEN] | position.piece_bb[B_QUEEN]
phase = 24 - (popcount(knights | bishops)
+ (popcount(rooks) * 2)
+ (popcount(queens) * 4))
phase = ((phase * 256) + 12) // 24
score_mg = 0
score_eg = 0
# Piece-square tables
score_mg += position.psq_score_mg[WHITE] - position.psq_score_mg[BLACK]
score_eg += position.psq_score_eg[WHITE] - position.psq_score_eg[BLACK]
# Evaluate material
material_score_mg, material_score_eg = self.evaluate_material(position)
score_mg += material_score_mg
score_eg += material_score_eg
# Evaluate pawns
pawn_score_mg, pawn_score_eg = self.evaluate_pawns(position)
score_mg += pawn_score_mg
score_eg += pawn_score_eg
# Mobility
mobility_bb = knights | bishops | rooks | queens
mobility_score_mg, mobility_score_eg = self.evaluate_mobility(position, mobility_bb)
score_mg += mobility_score_mg
score_eg += mobility_score_eg
# King safety
w_king_score_mg, w_king_score_eg = self.get_king_safety(position, WHITE)
b_king_score_mg, b_king_score_eg = self.get_king_safety(position, BLACK)
score_mg += w_king_score_mg - b_king_score_mg
score_eg += w_king_score_eg - b_king_score_eg
# Interpolate between midgame and endgame score based on phase
score = ((score_mg * (256 - phase)) + (score_eg * phase)) // 256
# Return score from current player's perspective + bonus for the side to move
return score + 28 if position.colour == WHITE else -score + 28
def test_trim(self):
for flags in xrange(16):
pn = MemoryPatriciaAuthTree()
pn.update((k, v) for k, v in six.iteritems(SCENARIOS[flags])
if k != 'hash_')
pn2 = MemoryPatriciaAuthTree()
pn2.update(pn)
res = pn2.trim(['abc'])
self.assertEqual(res, gmpy2.popcount(flags >> 1))
del pn2.hash
self.assertEqual(pn2.hash, SCENARIOS[flags]['hash_'], flags)
self.assertEqual(pn2.size, gmpy2.popcount(flags))
self.assertEqual(pn2.length, gmpy2.popcount(flags & 1))
if pn2.children:
self.assertEqual(pn2.children[0].size,
gmpy2.popcount(flags) - (flags & 1))
self.assertEqual(pn2.children[0].length, 0)
self.assertTrue(pn2.children[0].pruned)
pn3 = MemoryPatriciaAuthTree()
pn3.update(pn)
res = pn3.trim([Bits(bytes='abc\x00', length=25)])
self.assertEqual(res, gmpy2.popcount(flags >> 2))
del pn3.hash
self.assertEqual(pn3.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags))
self.assertEqual(pn3.length, gmpy2.popcount(flags & 3))
def count(number: int) -> int:
"""Count 1s in a binary number
Args:
number (int): binary number
Returns:
int: count
"""
return gmpy2.popcount(number)
def test_add_rule_2items(self, search_parameters,
generate_input_dataframe_two_target_normal,
generate_subgroup_2subgroups):
data = generate_input_dataframe_two_target_normal
input_target_model, input_max_depth, input_beam_width, input_minsupp, input_max_rules, input_alpha_gain = search_parameters
subgroup2add1, subgroup2add2 = generate_subgroup_2subgroups
input_task = "discovery"
output_ruleset = GaussianRuleList(data, input_task, input_max_depth,
input_beam_width, input_minsupp,
input_max_rules, input_alpha_gain)
output_ruleset.add_rule(subgroup2add1, data)
output_ruleset.add_rule(subgroup2add2, data)
expected_number_instances = data.number_instances
expected_bitset_uncovered = mpz()
expected_bitset_covered = bit_mask(100000)
expected_number_rules = 2
expected_length_model = universal_code_integers(2) + \
universal_code_integers(1) +uniform_combination_code(1, 2) +\
universal_code_integers_maximum(1, 2) + uniform_code(10)+ \
universal_code_integers(1) + uniform_combination_code(1, 2) + \
universal_code_integers_maximum(1, 1) + uniform_code(2)
actual_numberinstances1 = popcount(output_ruleset.subgroups[0].bitarray) + \
popcount(output_ruleset.subgroups[1].bitarray &~ output_ruleset.subgroups[0].bitarray) + \
popcount(output_ruleset.bitset_uncovered)
actual_numberinstances2 = output_ruleset.support_covered + output_ruleset.support_uncovered
actual_numberinstances3 = popcount(output_ruleset.bitset_covered) + \
popcount(output_ruleset.bitset_uncovered)
actual_numberinstances4 = output_ruleset.subgroups[0].usage + output_ruleset.subgroups[1].usage +\
output_ruleset.default_rule_statistics.usage
assert expected_number_instances == actual_numberinstances1
assert expected_number_instances == actual_numberinstances2
assert expected_number_instances == actual_numberinstances3
assert expected_number_instances == actual_numberinstances4
assert expected_bitset_uncovered == output_ruleset.bitset_uncovered
assert expected_bitset_covered == output_ruleset.bitset_covered
assert expected_number_rules == output_ruleset.number_rules
assert expected_length_model == pytest.approx(
output_ruleset.length_model)
def generateTotients(n): print "Generating Totients" memory = Memory(n) while gmpy2.popcount(memory.unseen)!=0: # print bin(memory.unseen) memory.updateUnseen() exponentiated_list = buildExponents(memory) seen_times_exponentiated_list = buildSeenTimesExponent(memory,exponentiated_list) memory.seen |= (exponentiated_list|seen_times_exponentiated_list) # print bin(memory.seen) return memory.totients
def test_add_rule_itemnumeric(self, search_parameters,
generate_input_dataframe_two_target_normal,
generate_subgroup_oneitem_numeric):
data = generate_input_dataframe_two_target_normal
input_target_model, input_max_depth, input_beam_width, input_minsupp, input_max_rules, input_alpha_gain = search_parameters
subgroup2add = generate_subgroup_oneitem_numeric
input_task = "discovery"
output_ruleset = GaussianRuleList(data, input_task, input_max_depth,
input_beam_width, input_minsupp,
input_max_rules, input_alpha_gain)
output_ruleset.add_rule(subgroup2add, data)
expected_number_instances = data.number_instances
expected_bitset_uncovered = indexes2bitset(
[i for i in range(expected_number_instances) if i > 16666])
expected_bitset_covered = indexes2bitset(
[i for i in range(expected_number_instances) if i < 16666 + 1])
expected_number_rules = 1
expected_length_model = universal_code_integers(1) + universal_code_integers(1)+\
uniform_combination_code(1, 2) + universal_code_integers_maximum(1,2)+ \
uniform_code(10)
actual_numberinstances1 = popcount(output_ruleset.subgroups[0].bitarray) +\
popcount(output_ruleset.bitset_uncovered)
actual_numberinstances2 = output_ruleset.support_covered + output_ruleset.support_uncovered
actual_numberinstances3 = popcount(output_ruleset.bitset_covered) +\
popcount(output_ruleset.bitset_uncovered)
actual_numberinstances4 = output_ruleset.subgroups[
0].usage + output_ruleset.default_rule_statistics.usage
assert expected_number_instances == actual_numberinstances1
assert expected_number_instances == actual_numberinstances2
assert expected_number_instances == actual_numberinstances3
assert expected_number_instances == actual_numberinstances4
assert expected_bitset_uncovered == output_ruleset.bitset_uncovered
assert expected_bitset_covered == output_ruleset.bitset_covered
assert expected_number_rules == output_ruleset.number_rules
assert expected_length_model == pytest.approx(
output_ruleset.length_model)
def __init__(self, name, num, truthtable):
self.num = num
self.name = name
self.tt = truthtable
# subtract 1 to remove leading 1
self.cardinality = truthtable.num_digits(2) - 1
self.captured = gmpy2.popcount(truthtable) - 1
# if more than half the samples are captured
if labels and self.captured > 0:
self.corr = gmpy2.popcount(self.tt & labels[1].tt) - 1
if self.corr >= (self.captured / 2):
self.predict = 1
self.correct = self.corr / float(self.captured)
else:
self.predict = 0
self.correct = (self.captured - self.corr) / \
float(self.captured)
else:
self.predict = 1
self.correct = 0
self.corr = 0
def set_mu(self,new_mu):
'''
update the value of mu in the Hamiltonian
:param new_mu: new value of mu
'''
# Compute the modification on the diagonal of H
delta_mu = self.mu-new_mu
#compute the dimension of the hamiltonian
n=2*len(self.impurity_index)
fock_dim=2**(2*n)
for i in np.arange(fock_dim):
# update each diagonal element of H according to the number of electrons
self.H[i,i]+=delta_mu*gmpy2.popcount(int(i))
self.mu=new_mu
def compare_bin15(large, small, mism):
import gmpy2
mycode = {'A': b'1000', 'C': b'0100', 'G': b'0010', 'T': b'0001'}
large_str = b''.join(mycode[c] for c in large)
small_str = b''.join(mycode[c] for c in small)
small_num = int(small_str, 2)
S = len(small)
out = []
for i in range(len(large) - S + 1):
large_num = int(large_str[4 * i : 4 * (i + S)], 2)
and_num = small_num & large_num
if gmpy2.popcount(and_num) >= S - mism:
out.append(i)
return out
def popcount(x):
"""
Efficient methods for counting the on-bits in an integer
It uses 17 arithmetic operations.
"""
# x -= (x >> 1) & m1 # put count of each 2 bits into those 2 bits
# x = (x & m2) + ((x >> 2) & m2) # put count of each 4 bits into those 4 bits
# x = (x + (x >> 4)) & m4 # put count of each 8 bits into those 8 bits
# x += x >> 8 # put count of each 16 bits into their lowest 8 bits
# x += x >> 16 # put count of each 32 bits into their lowest 8 bits
# x += x >> 32 # put count of each 64 bits into their lowest 8 bits
# return x & 0x7f
# Using library
return gmpy2.popcount(x)
def build_lookuptable(self):
""" Build a clever basis """
j_down = 0
for n_down in range(0, self.nb_electrons + 1):
nb_states = special.binom(self.nb_flavors / 2 * self.nb_sites,
self.nb_electrons - n_down)
for down_part in range(
0, int(pow(2, self.nb_flavors / 2 * self.nb_sites))):
j_up = 0
if gmpy2.popcount(down_part) == n_down:
for up_part in range(
0, int(pow(2,
self.nb_flavors / 2 * self.nb_sites))):
if gmpy2.popcount(
up_part) == self.nb_electrons - n_down:
self.J_up[up_part] = j_up
self.J_down[down_part] = j_down
self.J[int(j_up + j_down)] = pow(
2, self.nb_flavors / 2 *
self.nb_sites) * down_part + up_part
j_up += 1
j_up = 0
j_down += nb_states
def build_look_up_table(self,nb_sites):
'''
Build a look up tables to index the states in occupation representation
J(i) is the binary representation of the i-th state
Starting with the i-th state, its index can be found by computing (J_up(int(i_up))+J_down(int(i_down)))
:return: J J_up and J_down
'''
L = nb_sites
N = nb_sites # todo : custum number of electrons
n_states_per_spin = 2 ** (L)
J_up = np.zeros([n_states_per_spin],dtype="int")
J_down = np.zeros([n_states_per_spin],dtype="int")
J = np.zeros([int(scipy.misc.comb(2 * L, N))],dtype="int")
j_down = int(0) # First runner
for n_down in np.arange(N+1):
n_up=N-n_down
n_states_up=scipy.misc.comb(L,n_up)
j_up=int(0)
for down_part in np.arange (n_states_per_spin):
down_part=int(down_part)
n_down_electrons = gmpy2.popcount(down_part)
if n_down_electrons == n_down:
for upper_part in np.arange(n_states_per_spin):
upper_part=int(upper_part)
n_up_electrons = gmpy2.popcount(upper_part)
if (n_up_electrons==n_up):
J_up[upper_part]=j_up
J_down[down_part]=j_down
J[j_down+j_up]=n_states_per_spin*upper_part+down_part
j_up+=1
j_up=int(0)
j_down+=int(n_states_up)
return J,J_up,J_down
def add_rule(self, subgroup2add, tid_bitsets, attributes):
self.number_rules += 1
tid_cand = subgroup2add.bitset
self.bitset_covered = self.bitset_covered | tid_cand
self.support_covered = popcount(self.bitset_covered)
self.bitset_uncovered = self.bitset_uncovered & ~tid_cand
self.support_uncovered = popcount(self.bitset_uncovered)
self.bitset_rules.append(tid_cand)
self.antecedent_raw.append(subgroup2add.pattern)
self.statistic_rules.append(subgroup2add.statistic)
# IN CLASSIFICATION CASE EVERYTHING HAS TO BE UPDATED!
self.default_statistic["usage"] = self.support_uncovered
if self.task == "classification":
aux_tid = xmpz(self.bitset_uncovered)
idx_bitsdef = list(aux_tid.iter_set())
values_default = self.target_values[idx_bitsdef]
self.default_mean["mean"] = np.mean(values_default)
self.default_variance["variance"] = np.var(values_default)
# SHOULD BE REMOVED LATER ON
support = popcount(tid_cand)
self.support_rules.append(support)
self.add_pattern4prediction(subgroup2add.pattern, attributes)
self.consequent_description.append(
self.add_description_consequent(subgroup2add))
self.consequent_lastrule_description = self.add_consequent_lastrule()
self.add_description_antecedent(subgroup2add.pattern, attributes)
self.length_model = compute_length_model(self)
self.length_data = compute_length_data[self.target_type](self)
self.constant = delta_data_const[self.target_type](self)
if self.length_original > 0:
self.length_ratio = (self.length_data +
self.length_model) / self.length_original
elif self.length_original < 0:
self.length_ratio = self.length_original / (self.length_data +
self.length_model)
return self
def play_out(self, pb, ob, mp):
# pb,obが返されるのでob,pbに代入して同時に入れ替える
ob, pb = Play().put_turn(pb, ob, mp)
teban = 0
while True:
if not Play().legal_board(pb, ob):
pb, ob = ob, pb
teban ^= 1
if not Play().legal_board(pb, ob):
ps = popcount(pb) # player_stone
os = popcount(ob) # opponent_stone
if teban: # 手番が渡されたときと同じ
if ps >= os:
return 1
elif ps < os:
return 0
else: # 手番が渡されたときと異なる
if os >= ps:
return 1
elif os < ps:
return 0
mp = Move().rand_move(pb, ob)
ob, pb = Play().put_turn(pb, ob, mp)
teban ^= 1
def test_prune(self):
for flags in xrange(16):
pn = MemoryPatriciaDict()
old_items = set((k,v) for k,v in six.iteritems(SCENARIOS[flags]) if k != 'hash_')
pn.update(old_items)
for idx,scenario in enumerate(SCENARIOS):
if idx|flags != flags or idx&flags != idx:
continue
new_items = set((k,v) for k,v in six.iteritems(scenario) if k != 'hash_')
pn2 = MemoryPatriciaDict()
pn2.update(pn)
pn3 = MemoryPatriciaDict()
pn3.update(pn)
pn4 = MemoryPatriciaDict()
pn4.update(pn)
for d in (pn, pn2, pn3, pn4):
self.assertEqual(d.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(d.size, gmpy2.popcount(flags))
self.assertEqual(d.length, gmpy2.popcount(flags))
keys = set()
for (k,v) in new_items:
pn2.prune([k])
pn3.prune(iter([k]))
keys.add(k)
pn4.prune(keys)
self.assertEqual(pn.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn.size, gmpy2.popcount(flags))
self.assertEqual(pn.length, gmpy2.popcount(flags))
for d in (pn2, pn3, pn4):
del d.hash
self.assertEqual(d.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(d.size, gmpy2.popcount(flags))
self.assertEqual(d.length, gmpy2.popcount(flags) - len(new_items))
self.assertEqual(set(d.items()), old_items - new_items)
for key,value in old_items:
if key in keys:
with self.assertRaises(KeyError):
d.prune([key])
else:
self.assertEqual(d[key], value)
for item in old_items:
if item in new_items:
self.assertEqual(d[item[0]], item[1])
else:
with self.assertRaises(KeyError):
d.prune([item[0]])
def test_trim(self):
for flags in xrange(16):
pn = MemoryPatriciaDict()
pn.update((k,v) for k,v in six.iteritems(SCENARIOS[flags]) if k != 'hash_')
pn2 = MemoryPatriciaDict()
pn2.update(pn)
res = pn2.trim(['abc'])
self.assertEqual(res, gmpy2.popcount(flags>>1))
del pn2.hash
self.assertEqual(pn2.hash, SCENARIOS[flags]['hash_'], flags)
self.assertEqual(pn2.size, gmpy2.popcount(flags))
self.assertEqual(pn2.length, gmpy2.popcount(flags&1))
if pn2.children:
self.assertEqual(pn2.children[0].size, gmpy2.popcount(flags) - (flags&1))
self.assertEqual(pn2.children[0].length, 0)
self.assertTrue(pn2.children[0].pruned)
pn3 = MemoryPatriciaDict()
pn3.update(pn)
res = pn3.trim([Bits(bytes='abc\x00', length=25)])
self.assertEqual(res, gmpy2.popcount(flags>>2))
del pn3.hash
self.assertEqual(pn3.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags))
self.assertEqual(pn3.length, gmpy2.popcount(flags&3))
neighbors = [list(set([i for nbhd in neighborhoods[s] for i in nbhd]) - {s}) for s in squares]
setneighbors = [set(neighbors[s]) for s in squares]
coordinates = dict((s, [9,9,9]) for s in squares)
for x in range(9):
for y in the_rows[x]:
coordinates[y][0] = x
for y in the_columns[x]:
coordinates[y][1] = x
for y in the_boxes[x]:
coordinates[y][2] = x
# TODO This is a mess. Fix it.
tuples = [[] for n in range(10)]
for x in range(2**9):
p = gmpy2.popcount(x)
tuples[p].append(x)
singles = tuples[1]
values = dict((v, list({s & v for s in singles} - {0})) for v in range(2**9))
valuesets = dict((v, {s & v for s in singles} - {0}) for v in range(2**9))
methodnames = ['naked singles', 'naked doubles', 'hidden singles', 'hidden doubles', 'hidden triples',
'hidden quadruples', 'intersectionremoval', 'x-wing', 'given clue']
methodcounter = [0 for dummy in methodnames]
# </editor-fold>
def initialize(v):
"""
:param v: String representation of a sudoku board.
def eval_board(board, gameover=False):
white_mask = board.occupied_co[chess.WHITE]
black_mask = board.occupied_co[chess.BLACK]
material = ((gmpy2.popcount((board.pawns & white_mask)) - gmpy2.popcount((board.pawns & black_mask)))*1 +
(gmpy2.popcount((board.knights & white_mask)) - gmpy2.popcount((board.knights & black_mask)))*3 +
(gmpy2.popcount((board.bishops & white_mask)) - gmpy2.popcount((board.bishops & black_mask)))*3 +
(gmpy2.popcount((board.rooks & white_mask)) - gmpy2.popcount((board.rooks & black_mask)))*5 +
(gmpy2.popcount((board.queens & white_mask)) - gmpy2.popcount((board.queens & black_mask)))*9 +
(gmpy2.popcount((board.kings & white_mask)) - gmpy2.popcount((board.kings & black_mask)))*1000)
if gameover or abs(material) >= 9 or (gmpy2.popcount(white_mask) + gmpy2.popcount(black_mask)) < 9:
if board.is_checkmate():
if board.turn:
return -10000
else:
return 10000
return material
def test_update(self):
for flags in xrange(16):
pn = MemoryPatriciaDict()
pn.update((k,v) for k,v in six.iteritems(SCENARIOS[flags]) if k != 'hash_')
for idx,scenario in enumerate(SCENARIOS):
items = [(k,v) for k,v in six.iteritems(scenario) if k != 'hash_']
pn2 = MemoryPatriciaDict()
pn2.update(pn)
self.assertEqual(pn2.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn2.size, gmpy2.popcount(flags))
self.assertEqual(pn2.length, gmpy2.popcount(flags))
pn2.update(items)
self.assertEqual(pn2.hash, SCENARIOS[flags|idx]['hash_'])
self.assertEqual(pn2.size, gmpy2.popcount(flags|idx))
self.assertEqual(pn2.length, gmpy2.popcount(flags|idx))
pn3 = MemoryPatriciaDict()
pn3.update(pn)
self.assertEqual(pn3.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags))
self.assertEqual(pn3.length, gmpy2.popcount(flags))
pn3.update(iter(items))
self.assertEqual(pn3.hash, SCENARIOS[flags|idx]['hash_'])
self.assertEqual(pn3.size, gmpy2.popcount(flags|idx))
self.assertEqual(pn3.length, gmpy2.popcount(flags|idx))
pn4 = MemoryPatriciaDict()
pn4.update(pn)
self.assertEqual(pn4.hash, SCENARIOS[flags]['hash_'])
self.assertEqual(pn4.size, gmpy2.popcount(flags))
self.assertEqual(pn4.length, gmpy2.popcount(flags))
pn4.update(**dict(items))
self.assertEqual(pn4.hash, SCENARIOS[flags|idx]['hash_'])
self.assertEqual(pn4.size, gmpy2.popcount(flags|idx))
self.assertEqual(pn4.length, gmpy2.popcount(flags|idx))
def get_mobility(self, player):
valid_moves = self.__valid_moves(player)
move_in_all_dir = 0
for vm in valid_moves.values():
move_in_all_dir |= vm
return gmpy2.popcount(move_in_all_dir)