def regroup(l):
for sub in l:
flattened = func.flatten(sub)
if len(set(flattened)) == 1:
grouped.append(''.join(flattened))
elif type(sub) == list:
regroup(sub)
def _inference(self, X, keep_prob):
h = F.max_pool(F.activation(F.conv(X, 64)))
h = F.max_pool(F.activation(F.conv(h, 128)))
h = F.max_pool(F.activation(F.conv(h, 256)))
h = F.activation(F.dense(F.flatten(h), 1024))
h = F.dense(h, self._num_classes)
return tf.nn.softmax(h)
def _inference(self, X, keep_prob):
h = F.max_pool(F.activation(F.conv(X, 64)))
h = F.max_pool(F.activation(F.conv(h, 128)))
h = F.max_pool(F.activation(F.conv(h, 256)))
h = F.activation(F.dense(F.flatten(h), 1024))
h = F.dense(h, self._num_classes)
return h
def __init__(self,nbr,load_file):
"""
Fonction d'initialisation
Lit le texte pour enumerer les mots
"""
RNN_lettre.__init__(self,nbr,load_file)
self.vocab_lettre_size = self.vocab_size
self.text_file.seek(0)
m = 0
self.data_mots_origin = []
while 1:
ch = self.text_file.readline()
if ch == "":
break
# conversion de la chaine lue en une liste de mots :
li = ch.split()
# separation des caracteres speciaux "colle" au mot
for charspe in self.list_charspe:
li[:] = [replacePonctuation(charspe,word) for word in li[:]]
li = list(flatten(li))
while charspe in li:
li.remove(charspe)
while '' in li:
li.remove('')
#print li
# print li
# totalisation des mots :
m = m + len(li)
for mot in li:
self.data_mots_origin.append(mot)
self.text_file.close()
self.mots = []
self.mots = list(set(self.data_mots_origin))
self.data_size, self.vocab_size = len(self.data_mots_origin), len(self.mots)
print "Ce fichier texte contient un total de %s mots" % (m)
print "et contient ",len(self.mots), " mots unique"
self.mots_to_ix = { ch:i for i,ch in enumerate(self.mots) }
self.ix_to_mots = { i:ch for i,ch in enumerate(self.mots) }
# matrice pour calculer distance entre les mots
self.matrice_mot = np.zeros((self.vocab_size, self.vocab_lettre_size))
for i,mot in enumerate(self.mots):
#print i," : ",mot
for car in mot:
#print car
ix = self.char_to_ix[car]
self.matrice_mot[i][ix] += 1
def crossover(dna, temperature, cross_prob, data):
dna = list(dna)
random.shuffle(dna)
half = int(len(dna)/2)
# L = range(len(dna[0]))
chrom_l = len(dna[0])
cross_dna = flatten(list(map(
lambda x, y: pmx_crossover(x, y, chrom_l, cross_prob, data),
dna[:half], dna[half:]
)))
genome = list(map(lambda x: eval_distance(x, data), cross_dna))
# +2 because it needs to be at least len 2 for a reverse
mut_len = round(chrom_l * (temperature/100)) + 2
return list(map(
lambda x: mutation(x, chrom_l, mut_len, temperature, data), genome
))
def update_species(self, new_creature: Creature = None) -> None:
"""
Generates a dictionary with a creature as a key and all creatures in the population that are similar to it,
including itself. This function is called every time a creature is born. The creature representing a species
can die, but it will still represent that species until the SPECIES dies.
"""
# Check genetic distance from all species representatives, if it is smaller than the threshold catalogue the,
# creature into that species. If no matching species was found then make a new one with creature as the rep.
if new_creature is None:
# Find all creatures not catalogued into a species.
all_creatures = flatten(list(self.species.values()))
uncatalogued_creatures = [creature for creature in self.population if creature not in all_creatures]
else:
# Can save time if new creature is specified
uncatalogued_creatures = [new_creature]
while uncatalogued_creatures:
creature = choice(uncatalogued_creatures)
self.catalogue_creature(creature)
uncatalogued_creatures.remove(creature)
def load_moka_data(plt_show = False):
"""
Function to load informations from a single moka run
Input:
- lenses_vec [{},...] : list of dictionaries with the lens model
- args namespace : name space with float 'source_final_z'
- plt_show str : lenstool file name
Output:
- NONE
"""
if os.path.exists("axes.d") and os.path.exists("projection.d"):
print ".d files exist"
nfw_info_path = "nfw_info.dat"
nfw_data = { "kappa_s" : \
fc.extract_parameter(nfw_info_path, "kappa_s")[0][0], \
"cl" : fc.extract_parameter(nfw_info_path, "cl")[0][0] \
}
sis_info_path = "sis_info.dat"
if os.path.exists(sis_info_path):
sis_data_tmp = fc.flatten( fc.extract_parameter(sis_info_path, "cl") )
else:
sis_data_tmp = []
sis_data = []
i = 0
while i < len(sis_data_tmp):
sis_data.append(float(sis_data_tmp[i]))
i = i + 2
if os.path.exists(sis_info_path):
stat_info_path = "satellites/satinfo.0.sub"
stat_data = np.loadtxt(stat_info_path, unpack = True)
else:
stat_data = [[]]
main_info_path = "info_haloes.dat"
main_data = np.loadtxt(main_info_path, unpack = True)
rvir0 = fc.extract_parameter( "rvir0.dat", "Rvir0")[0][0]
if plt_show:
plt.figure(1, figsize=(8, 8))
plt.hist( np.log10(stat_data[0]), log = True, bins = 15 )
plt.xlabel(r"$\rm \log_{10}(Mass)$")
plt.xlim( min(np.log10(stat_data[0])), max(np.log10(stat_data[0])) )
plt.ylabel(r"$\rm counts$")
plt.title(r"$\rm Substructure \; Mass \; Distribution$")
plt.show()
plt.subplot(1, 1, 1).set_aspect(1)
size_1 = stat_data[0]/max(stat_data[0])*50 + 1
axis_limit = max( 1.075*max(stat_data[2]), 1.075*max(stat_data[3]) )
plt.scatter(stat_data[2], stat_data[3], s = size_1 , color = "b", \
edgecolors = 'none')
plt.axis([-axis_limit, axis_limit, -axis_limit, axis_limit])
plt.xlabel("$x$")
plt.ylabel("$y$")
plt.show()
#plt.hist(np.log10(sis_data), log = True)
#plt.show()
ell = 0.0
file_gravlens = open('gravlens.gravlens', 'w')
file_gravlens.write("startup " + str(len(stat_data[0]) + 1) + " 1\n")
file_gravlens.write(" nfw " + \
str(float(nfw_data["kappa_s"])/(1.0 - ell)) + \
" 0.0 0.0 " + str(ell) + " 0.0 0.0 0.0 " + \
str(float(nfw_data["cl"])/(1.0 - ell)) + " 0.0 0.0\n")
for i in range(len(sis_data)):
file_gravlens.write( " alphapot " + str(sis_data[i]) + " " + \
str(stat_data[2][i]) + " " + str(stat_data[3][i]*1.4) + \
" 0.0 0.0 0.0 0.0 0.0 0.0 1.0\n")
for i in range(len(sis_data) + 1):
file_gravlens.write( " 0 0 0 0 0 0 0 0 0 0\n")
file_gravlens.write( "plotdef1 pot_gl.txt -" + rvir0 + " " + rvir0 + \
" 256 -" + rvir0 + " " + rvir0 + " 256\n" )
#file_gravlens.write( "plotkappa kappa_gl.fits 3 -" + rvir0 + " " + rvir0 + \
# " 512 -" + rvir0 + " " + rvir0 + " 512\n" )
file_gravlens.write( "plotcrit crit.dat" )
file_gravlens.close()
def _truncation(dna, local_array, n=.5):
assert local_array % 2 == 0, "CANNOT TRUNCATE UNEAVEN DNA"
dna = dna[:int(local_array*n)]
# this doubles and maintains fitness ordering of chroms
return flatten(zip(dna, dna))
def getattrs_by_filter(self, key, value,
attrlist=None,
base=None,
pageSize=1000,
compare='=',
addt_filter=''):
'''Search AD by attribute.
:param attrlist: The attributes desired (None for all)
:type attrlist: list
:param compare: Comparison, valid operators: =, >=, <=
(lexicographical)
:return: A list of result dictionaries.
Examples:
>>> mldapObj.getattrs_by_filter("sAMAccountName",
"wimpy")[0]['sAMAccountName']
'wimpy'
>>> mldapObj.getattrs_by_filter("sAMAccountName",
"wimpy")[0]['objectClass']
['top', 'person', 'organizationalPerson', 'user']
'''
if base is None:
base = self.LDAP_USER_BASE
search = None
# To handle searches for None values (to answer who DOESN'T
# have an e-mail attribute set?), the search filter should use
# the not-present operator: (!attribute_name=*) to test for
# the absence of an attribute
if value is None:
search = ("(&(!(objectClass=computer))"
"(!(objectClass=organizationalUnit))"
"(!(%s=*))%s)") % (str(key),
addt_filter)
elif key == 'objectGUID':
search = "(&(!(objectClass=computer))(%s%s%s)%s)" % (
str(key),
compare,
ldap.filter.escape_filter_chars(str(value)),
addt_filter)
else:
search = "(&(!(objectClass=computer))(%s%s%s)%s)" % (
str(key),
ldap.filter.escape_filter_chars(compare),
str(value),
addt_filter)
lc = ldap.controls.SimplePagedResultsControl(
ldap.LDAP_CONTROL_PAGE_OID, True, (pageSize, ''))
msgid = self.ldap_client.search_ext(
base,
ldap.SCOPE_SUBTREE,
search,
serverctrls=[lc],
attrlist=attrlist)
results = []
pages = 0
while True:
pages += 1
rtype, rdata, rmsgid, serverctrls = self.ldap_client.result3(msgid)
# Each result tuple (rdata) is of the form (dn, attrs),
# where dn is a string containing the DN (distinguished
# name) of the entry, and attrs is a dictionary containing
# the attributes associated with the entry. The keys of
# attrs are strings, and the associated values are lists
# of strings.
for (dn, entry) in rdata:
if dn is not None:
results.append(entry)
pctrls = [
c
for c in serverctrls
if c.controlType == ldap.LDAP_CONTROL_PAGE_OID
]
if pctrls:
est, cookie = pctrls[0].controlValue
if cookie:
lc.controlValue = (pageSize, cookie)
msgid = self.ldap_client.search_ext(
base,
ldap.SCOPE_SUBTREE,
search,
serverctrls=[lc],
attrlist=attrlist)
else:
break
else:
print "Warning: Server ignores RFC 2696 control."
break
for result in results:
for attr in result:
result[attr] = flatten(result[attr])
return results
plt.axis('off')
plt.subplot(236)
plt.imshow(mixture2_hvs[:,:,2], cmap = 'hsv')
plt.axis('off')
plt.tight_layout()
#plt.savefig("mixtures_hsv_set5_theta30.png")
plt.show()
"""X1, W1 = whiten_projection(mixture_channel_1)
B1 = np.dot(W1, mixing_matrix)
X2, W2 = whiten_projection(mixture_channel_2)
B2 = np.dot(W2, mixing_matrix)
X3, W3 = whiten_projection(mixture_channel_3)
B3 = np.dot(W3, mixing_matrix)"""
stacked_channel_h_mixtures = flatten(mixture1_hvs[:,:,0], mixture2_hvs[:,:,0])
stacked_channel_s_mixtures = flatten(mixture1_hvs[:,:,1], mixture2_hvs[:,:,1])
stacked_channel_v_mixtures = flatten(mixture1_hvs[:,:,2], mixture2_hvs[:,:,2])
stacked_channel_h_source = flatten(source1_hsv[:,:,0], source2_hsv[:,:,0])
stacked_channel_s_source = flatten(source1_hsv[:,:,1], source2_hsv[:,:,1])
stacked_channel_v_source = flatten(source1_hsv[:,:,2], source2_hsv[:,:,2])
mixture_channel_list_hsv = [stacked_channel_h_mixtures, stacked_channel_s_mixtures, stacked_channel_v_mixtures]
source_channel_list_hsv = [stacked_channel_h_source, stacked_channel_s_source, stacked_channel_v_source]
for i in np.arange(3):
X_i, W_i = whiten_projection(mixture_channel_list_hsv[i])
B_i = np.dot(W_i, mixing_matrix)
(sdr_ref, sir_ref, sar, perm) = mmetrics.bss_eval_sources(source_channel_list_hsv[i], X_i)
print('The mean value of the reference SDR is: ', np.mean(sdr_ref), perm)
if np.array_equal(perm, [[1],[0]]):
# print "Hello world!"
parser = argparse.ArgumentParser(description = \
"Add a new column to a table.", \
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("in_file", help="File name", type=str)
parser.add_argument("--position", help = "Position for the new column.", \
type = int, default = 0)
parser.add_argument("--precision", help = "Number of decimal cases.", \
type = int, default = 6)
parser.add_argument("--value", help = "Value to be added.", \
type = float, default = 0.0)
args = parser.parse_args()
data = np.loadtxt(args.in_file, unpack=False)
fmt = ""
for i in range(len(data[0]) + 1):
fmt = fmt + "%." + str(args.precision) + "E "
fmt = fmt[:len(fmt) - 2]
for i in range(len(data)):
print fmt % tuple(fc.flatten([data[i][0:args.position], args.value, \
data[i][args.position:len(data[i])]]))
def test_flatten_ok():
result = list(functions.flatten([1, [2, 3, [4, 5]]]))
assert [1, 2, 3, 4, 5] == result
def test_flatten_non_iterable_return_error():
with pytest.raises(TypeError):
functions.flatten()
def setup_iterables(path):
"""
Sets up the iterables to work with and populates them with the data located
at *path*
"""
abs_path = os.path.join(c.PRE_PATH, path)
if_time_scn_ch = [[[channel] for channel in range(c.N_CHAN)]
for scenario in range(c.N_SCN)]
# Packet rate per scenario
packet_rate_scn = [[] for scenario in range(c.N_SCN)]
# Variance per scenario
variance_scn = [[] for scenario in range(c.N_SCN)]
# Generate a list that includes the interframe time for all channels
if_vector = [[] for i in range(c.N_SAMPS * c.N_SCN)]
try:
for scenario in range(c.N_SCN):
for channel in range(c.N_CHAN):
if_time_scn_ch[scenario][channel] = sp.fromfile(
open(
os.path.join(
abs_path,
"interframe_time_ch_{}_scn_{}.dat".format(
channel + 1, scenario))),
dtype=sp.float32)
packet_rate_scn[scenario] = sp.fromfile(open(
os.path.join(abs_path,
"packet_rate_scn_{}.dat".format(scenario))),
dtype=sp.float32)
variance_scn[scenario] = sp.fromfile(open(
os.path.join(abs_path,
"variance_scn_{}.dat".format(scenario))),
dtype=sp.float32)
except IOError as e:
print("Error trying to access path: ", e)
raise
# Populate the conglomerated interframe_time list
for scn in range(c.N_SCN):
for i in range(c.N_SAMPS):
for chan in range(c.N_CHAN):
if_vector[i + c.N_SAMPS * scn].append(
if_time_scn_ch[scn][chan][i])
# Generate label list
labels = [i for i in range(c.N_SCN) for n in range(c.N_SAMPS)]
# Generate a list that includes all data in a list per frames
data_nested = []
# first generate a long list that includes the packet_rates one scenario
# after the other, and the same for the variances
# packet_rate = [scn0, scn1, ..., scn9]
# len(packet_rate) = N_SAMPS * N_SCN
packet_rate = []
variance = []
for scn in range(c.N_SCN):
for i in range(c.N_SAMPS):
packet_rate.append(packet_rate_scn[scn][i])
variance.append(variance_scn[scn][i])
data_nested = list(zip(if_vector, packet_rate, variance))
# Until this point 'data' is a nested list. It needs to be flattened
# to use it with sci-kit
# TODO: just don't generate it nested and save this method...
data = [[] for i in range(len(data_nested))]
for i in range(len(data_nested)):
data[i] = list(fun.flatten(data_nested[i]))
return data, labels
plt.imshow(mixture2_lab[:, :, 1], cmap='RdYlGn')
plt.axis('off')
plt.subplot(236)
plt.imshow(mixture2_lab[:, :, 2])
plt.axis('off')
plt.tight_layout()
#plt.savefig("mixtures_lab_set5_theta30.png")
plt.show()
"""X1, W1 = whiten_projection(mixture_channel_1)
B1 = np.dot(W1, mixing_matrix)
X2, W2 = whiten_projection(mixture_channel_2)
B2 = np.dot(W2, mixing_matrix)
X3, W3 = whiten_projection(mixture_channel_3)
B3 = np.dot(W3, mixing_matrix)"""
stacked_channel_l_mixtures = flatten(mixture1_lab[:, :, 0], mixture2_lab[:, :,
0])
stacked_channel_a_mixtures = flatten(mixture1_lab[:, :, 1], mixture2_lab[:, :,
1])
stacked_channel_b_mixtures = flatten(mixture1_lab[:, :, 2], mixture2_lab[:, :,
2])
stacked_channel_l_source = flatten(source1_lab[:, :, 0], source2_lab[:, :, 0])
stacked_channel_a_source = flatten(source1_lab[:, :, 1], source2_lab[:, :, 1])
stacked_channel_b_source = flatten(source1_lab[:, :, 2], source2_lab[:, :, 2])
mixture_channel_list_lab = [
stacked_channel_l_mixtures, stacked_channel_a_mixtures,
stacked_channel_b_mixtures
]
source_channel_list_lab = [
stacked_channel_l_source, stacked_channel_a_source,