def _parse_parameter_file(self):
super()._parse_parameter_file()
end = min(self.dimensionality + 1, 4)
self.geometry = "spectral_cube"
log_str = "Detected these axes: " + "%s " * len(self.ctypes)
mylog.info(log_str, *self.ctypes)
self.lat_axis = np.zeros((end - 1), dtype="bool")
for p in lat_prefixes:
self.lat_axis += np_char.startswith(self.ctypes, p)
self.lat_axis = np.where(self.lat_axis)[0][0]
self.lat_name = self.ctypes[self.lat_axis].split("-")[0].lower()
self.lon_axis = np.zeros((end - 1), dtype="bool")
for p in lon_prefixes:
self.lon_axis += np_char.startswith(self.ctypes, p)
self.lon_axis = np.where(self.lon_axis)[0][0]
self.lon_name = self.ctypes[self.lon_axis].split("-")[0].lower()
if self.lat_axis == self.lon_axis and self.lat_name == self.lon_name:
self.lat_axis = 1
self.lon_axis = 0
self.lat_name = "Y"
self.lon_name = "X"
self.spec_axis = 2
self.spec_name = "z"
self.spec_unit = ""
def function(famille, period):
period = period.start.period(u'year').offset('first-of')
depcom = famille('depcom', period)
return period, np.logical_or(startswith(depcom, '97'),
startswith(depcom, '98'))
def function(self, simulation, period):
period = period
depcom_holder = simulation.compute('depcom', period)
depcom = self.cast_from_entity_to_roles(depcom_holder)
depcom = self.filter_role(depcom, role = CHEF)
return period, startswith(depcom, '973')
def formula(menage, period):
depcom = menage('depcom', period.first_month)
departements_idf = [b'75', b'77', b'78', b'91', b'92', b'93', b'94', b'95']
in_idf = sum([startswith(depcom, departement_idf) for departement_idf in departements_idf])
rfr_declarants_principaux_du_menage = menage.members.has_role(FoyerFiscal.DECLARANT_PRINCIPAL) * menage.members.foyer_fiscal('rfr', period.n_2)
rfr = menage.sum(rfr_declarants_principaux_du_menage)
nb_members = menage.nb_persons()
bareme_idf = select(
[nb_members == 1, nb_members == 2, nb_members == 3, nb_members == 4, nb_members >= 5],
[select([rfr <= 19875, rfr <= 24194], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 29171, rfr <= 35510], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 35032, rfr <= 42648], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 40905, rfr <= 49799], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 46798 + ((nb_members - 5) * 5882), rfr <= 56970 + ((nb_members - 5) * 7162)], [2, 1], 0)])
bareme_out = select(
[nb_members == 1, nb_members == 2, nb_members == 3, nb_members == 4, nb_members >= 5],
[select([rfr <= 14360, rfr <= 18409], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 21001, rfr <= 26923], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 25257, rfr <= 32377], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 29506, rfr <= 37826], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 33774 + ((nb_members - 5) * 4257), rfr <= 43297 + ((nb_members - 5) * 5454)], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier)])
return where(in_idf, bareme_idf, bareme_out)
def mask_gaps(seqs, thresh=1.0):
"""Remove columns in an alignment when a certain fraction of sites
are gaps
Parameters
----------
seqs : dict
alignment
thresh : float between 0 and 1, option
fraction of gaps needed for column to be removed
Returns
-------
algn : dict
alignment with gapped columns removed
"""
import numpy
from numpy.core.defchararray import startswith
nams = list(seqs)
nseq = len(nams)
data = []
for n in nams:
data.append(list(seqs[n]))
data = numpy.array(data)
perc = numpy.sum(startswith(data, '-'), axis=0) / float(nseq)
cols = numpy.where(perc < thresh)[0]
data = data[:, cols]
algn = {}
for i, n in enumerate(nams):
algn[n] = ''.join(list(data[i, :]))
return algn
def formula(menage, period):
depcom = menage('depcom', period.first_month)
departements_idf = [b'75', b'77', b'78', b'91', b'92', b'93', b'94', b'95']
in_idf = sum([startswith(depcom, departement_idf) for departement_idf in departements_idf])
rfr_declarants_principaux_du_menage = menage.members.has_role(FoyerFiscal.DECLARANT_PRINCIPAL) * menage.members.foyer_fiscal('rfr', period.n_2)
rfr = menage.sum(rfr_declarants_principaux_du_menage)
nb_members = menage.nb_persons()
bareme_idf = select(
[nb_members == 1, nb_members == 2, nb_members == 3, nb_members == 4, nb_members >= 5],
[select([rfr <= 19875, rfr <= 24194], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 29171, rfr <= 35510], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 35032, rfr <= 42648], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 40905, rfr <= 49799], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 46798 + ((nb_members - 5) * 5882), rfr <= 56970 + ((nb_members - 5) * 7162)], [2, 1], 0)])
bareme_out = select(
[nb_members == 1, nb_members == 2, nb_members == 3, nb_members == 4, nb_members >= 5],
[select([rfr <= 14360, rfr <= 18409], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 21001, rfr <= 26923], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 25257, rfr <= 32377], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 29506, rfr <= 37826], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier),
select([rfr <= 33774 + ((nb_members - 5) * 4257), rfr <= 43297 + ((nb_members - 5) * 5454)], [TypesEligibiliteANAH.tres_modeste, TypesEligibiliteANAH.modestes], TypesEligibiliteANAH.a_verifier)])
return where(in_idf, bareme_idf, bareme_out)
def formula(individu, period, parameters):
params = parameters(
period).regions.occitanie.msa_midi_pyrenees_sud.aide_permis
montant = params.montant
depcom = individu.menage('depcom', period)
eligibilite_geographique = sum([
startswith(depcom, code_departement)
for code_departement in code_departements
])
allocataire_msa = individu(
'regime_securite_sociale',
period) == RegimeSecuriteSociale.regime_agricole
age = individu('age', period)
eligibilite_age = (age >= params.age.minimum) * (age <=
params.age.maximum)
quotient_familial = individu.foyer_fiscal(
'rfr', period.this_year) / 12 / individu.foyer_fiscal(
'nbptr', period.this_year)
eligibilite_quotient_familial = quotient_familial <= params.plafond_quotient_familial
return allocataire_msa * eligibilite_geographique * eligibilite_age * eligibilite_quotient_familial * montant
def change_template(self, ch: Chromosome, cluster_id: int, template_index: int):
# get the template at position index
template = ch.templates[cluster_id][template_index]
star_indexes = list()
non_star_indexes = list()
for index in range(0, template.get_length()):
if template.token[index] == '*':
star_indexes.append(index)
elif not (startswith(template.token[index], "[") or template.token[index] == '#spec#' or
re.match("\B\W\Z", template.token[index])):
non_star_indexes.append(index)
if random.random() <= 0.50:
if len(star_indexes) > 0:
index = random.choice(star_indexes)
message_index = random.choice(template.matched_lines)
message = self.chGenerator.messages[cluster_id][message_index]
template.token[index] = message.words[index]
else:
if len(non_star_indexes) > 0:
index = random.choice(non_star_indexes)
clone = Template(template.token[:])
clone.token[index] = '*'
compute_matched_lines(self.chGenerator.messages, clone)
if len(clone.matched_lines) > len(template.matched_lines):
template.token[index] = '*'
template.set_changed(True)
compute_matched_lines(self.chGenerator.messages, template)
def generate_template_from_line(self, cluster_id: int, rand_value: int):
""" Generates a Template from a cluster
"""
template = self.messages[cluster_id][rand_value].words[:]
if len(template) > 1:
contains_star = False
for word in template:
if word == "#spec#":
contains_star = True
break
if not contains_star:
modifiable_indexes = list()
for index in range(0, len(template)):
if not (startswith(template[index], "[")
or re.match("\B\W\Z", template[index])):
modifiable_indexes.append(index)
if len(modifiable_indexes) > 0:
index = random.choice(modifiable_indexes)
template[index] = '*'
t = Template(template)
compute_matched_lines(self.messages, t)
return t
def function(self, simulation, period):
period = period
depcom_holder = simulation.compute('depcom', period)
depcom = self.cast_from_entity_to_roles(depcom_holder)
depcom = self.filter_role(depcom, role=CHEF)
return period, startswith(depcom, '976')
def formula_2021_07_21(individu, period, parameters):
age = individu('age', period)
criteres_age = parameters(period).regions.hauts_de_france.aide_permis.age
eligibilite_age = (criteres_age.minimum <= age) * (age <= criteres_age.maximum)
depcom = individu.menage('depcom', period)
eligibilite_geographique = sum([startswith(depcom, code_departement) for code_departement in code_departements])
plafond_ressources = parameters(period).regions.hauts_de_france.aide_permis.plafond_ressources
rfr = individu.foyer_fiscal('rfr', period.n_2)
nbptr = individu.foyer_fiscal('nbptr', period.n_2)
activite_eligible = (individu('activite', period) == TypesActivite.chomeur) + (individu('activite', period) == TypesActivite.inactif)
stagiaire = individu('stagiaire', period)
apprenti = individu('apprenti', period)
eligibilite_situation = activite_eligible + stagiaire + apprenti
statut_marital = individu('statut_marital', period)
eligibilite_couple = (
((statut_marital == TypesStatutMarital.marie) + (statut_marital == TypesStatutMarital.pacse)) *
plafond_ressources.base_personne_couple >= rfr
)
eligibilite_autonome = (
(statut_marital == TypesStatutMarital.celibataire) *
plafond_ressources.base_personne_autonome >= max_(0, rfr / nbptr)
)
return eligibilite_age * eligibilite_geographique * eligibilite_situation * (eligibilite_autonome + eligibilite_couple)
def _parse_parameter_file(self):
super(SpectralCubeFITSDataset, self)._parse_parameter_file()
self.geometry = "spectral_cube"
end = min(self.dimensionality+1,4)
self.spec_axis = np.zeros(end-1, dtype="bool")
for p in spec_names.keys():
self.spec_axis += np_char.startswith(self.ctypes, p)
self.spec_axis = np.where(self.spec_axis)[0][0]
self.spec_name = spec_names[self.ctypes[self.spec_axis].split("-")[0][0]]
# Extract a subimage from a WCS object
self.wcs_2d = self.wcs.sub(["longitude", "latitude"])
self._p0 = self.wcs.wcs.crpix[self.spec_axis]
self._dz = self.wcs.wcs.cdelt[self.spec_axis]
self._z0 = self.wcs.wcs.crval[self.spec_axis]
self.spec_unit = str(self.wcs.wcs.cunit[self.spec_axis])
if self.spectral_factor == "auto":
self.spectral_factor = float(max(self.domain_dimensions[[self.lon_axis,
self.lat_axis]]))
self.spectral_factor /= self.domain_dimensions[self.spec_axis]
mylog.info("Setting the spectral factor to %f" % (self.spectral_factor))
Dz = self.domain_right_edge[self.spec_axis]-self.domain_left_edge[self.spec_axis]
dre = self.domain_right_edge
dre[self.spec_axis] = (self.domain_left_edge[self.spec_axis] +
self.spectral_factor*Dz)
self.domain_right_edge = dre
self._dz /= self.spectral_factor
self._p0 = (self._p0-0.5)*self.spectral_factor + 0.5
def mask_gaps(seqs, thresh=1.0):
"""
Removes columns in an alignment when a certain fraction
of sites are gaps. Default is 100% gaps or 1.
Parameters
----------
seqs : python dictionary
Returns
-------
algn : python dictionary
"""
import numpy
from numpy.core.defchararray import startswith
nams = seqs.keys()
nseq = len(nams)
data = []
for n in nams:
data.append(list(seqs[n]))
data = numpy.array(data)
perc = numpy.sum(startswith(data, '-'), axis=0) / float(nseq)
cols = numpy.where(perc < thresh)[0]
data = data[:, cols]
algn = {}
for i, n in enumerate(nams):
algn[n] = ''.join(list(data[i, :]))
return algn
def formula(individu, period):
age = individu('age', period)
depcom = individu.menage('depcom', period)
eligibilite_geographique = startswith(depcom, b'85')
eligible = eligibilite_geographique * (age >= 16) * (age <= 25)
return 800 * eligible
def formula(menage, period, parameters):
depcom = menage('depcom', period)
return sum(
[
startswith(depcom, str.encode(departement_idf))
for departement_idf in parameters(
period).geopolitique.departements_idf
]
) # TOOPTIMIZE: string encoding into bytes array should be done at load time
def formula(menage, period):
code_departements = [
b'16', b'17', b'19', b'23', b'24', b'33', b'40', b'47', b'64',
b'79', b'86', b'87'
]
depcom = menage('depcom', period)
return sum([startswith(depcom, code)
for code in code_departements]) > 0
def formula(individu, period):
age = individu('age', period)
activite = individu('activite', period)
depcom = individu.menage('depcom', period)
eligibilite_geographique = sum(
[startswith(depcom, code) for code in code_departements]) > 0
etudiant_eligible = (activite == TypesActivite.etudiant)
autre_eligible = (age >= 15) * (age <= 19) * (activite !=
TypesActivite.etudiant)
return eligibilite_geographique * (etudiant_eligible + autre_eligible)
def formula(menage, period):
depcom = menage('depcom', period)
in_paris_communes_limitrophes = sum([
depcom == commune_proche_paris
for commune_proche_paris in paris_communes_limitrophes
])
in_idf = sum([
startswith(depcom, departement) for departement in departements_idf
])
return select([in_paris_communes_limitrophes, in_idf], [
ZoneLogementSocial.paris_communes_limitrophes,
ZoneLogementSocial.ile_de_france,
],
default=ZoneLogementSocial.autres_regions)
def formula(individu, period, parameters):
params = parameters(period).regions.bretagne.msa_armorique.aide_permis
montant = params.montant
depcom = individu.menage('depcom', period)
eligibilite_geographique = sum([startswith(depcom, code_departement) for code_departement in code_departements])
allocataire_msa = individu('regime_securite_sociale', period) == RegimeSecuriteSociale.regime_agricole
age = individu('age', period)
eligibilite_age = age <= params.age.maximum
smic = parameters(period).marche_travail.salaire_minimum.smic
smic_brut_mensuel = smic.smic_b_horaire * smic.nb_heures_travail_mensuel
eligibilite_salaire = individu('salaire_de_base', period.last_3_months, options = [ADD]) / 3 / smic_brut_mensuel * 100 <= params.pourcentage_ressources_maximum_jeune
quotient_familial = individu.foyer_fiscal('rfr', period.this_year) / 12 / individu.foyer_fiscal('nbptr', period.this_year)
enfant_a_charge = individu('enfant_a_charge', period.this_year)
eligibilite_famillle = (quotient_familial <= params.plafond_quotient_familial) * enfant_a_charge
return eligibilite_geographique * allocataire_msa * eligibilite_age * (eligibilite_salaire + eligibilite_famillle) * montant
def formula(individu, period, parameters):
params = parameters(
period).regions.normandie.msa_haute_normandie.aide_permis
ars_params = parameters(
period
).prestations_sociales.prestations_familiales.education_presence_parentale.ars.ars_plaf
smic = parameters(period).marche_travail.salaire_minimum.smic
montant = params.montant
allocataire_msa = individu(
'regime_securite_sociale',
period) == RegimeSecuriteSociale.regime_agricole
enfant_a_charge = individu('enfant_a_charge', period.this_year)
alternant = individu('alternant', period)
depcom = individu.menage('depcom', period)
eligibilite_geographique = sum([
startswith(depcom, code_departement)
for code_departement in code_departements
])
age = individu('age', period)
eligibilite_age = (age >= params.age.minimum) * (age <=
params.age.maximum)
af_nbenf = individu.famille('af_nbenf', period)
plafond_ressources = ars_params.plafond_ressources * (
1 + af_nbenf * ars_params.majoration_par_enf_supp)
eligibilite_plafond_ressources = individu.foyer_fiscal(
'rfr', period.this_year) <= plafond_ressources
smic_brut_mensuel = smic.smic_b_horaire * smic.nb_heures_travail_mensuel
eligibilite_salaire = individu('salaire_de_base',
period) <= smic_brut_mensuel
return (
allocataire_msa + (enfant_a_charge * alternant)
) * eligibilite_geographique * eligibilite_age * eligibilite_plafond_ressources * eligibilite_salaire * montant
def formula(self, simulation, period):
period = period.start.period('year').offset('first-of')
city_code = simulation.calculate('city_code', period)
return np.logical_or(startswith(city_code, '97'),
startswith(city_code, '98'))
def find_axes(axis_names, prefixes):
x = 0
for p in prefixes:
y = np_char.startswith(axis_names, p)
x += np.any(y)
return x
def formula(menage, period, parameters):
depcom = menage('depcom', period)
return startswith(depcom, b'971')
def formula(menage, period):
return startswith(menage('depcom', period), b'22')
def formula(menage, period, parameters):
depcom = menage('depcom', period)
return startswith(depcom, '971')
def function(self, depcom):
return np.logical_or(startswith(depcom, '97'), startswith(depcom, '98'))
def function(self, simulation, period):
period = period.start.period(u'year').offset('first-of')
depcom = simulation.calculate('depcom', period)
return period, np.logical_or(startswith(depcom, '97'), startswith(depcom, '98'))
def function(self, simulation, period):
depcom = simulation.calculate('depcom', period)
return period, startswith(depcom, '973')
def function(famille, period):
depcom = famille('depcom', period)
return np.logical_or(startswith(depcom, '97'),
startswith(depcom, '98'))
def formula(menage, period):
depcom = menage('depcom', period)
return startswith(depcom, b'67')
def run(self) -> None:
# Load metadata
metadata: np.ndarray = None
meta_attrs: np.ndarray = None
metadata_file = os.path.join(am.paths().samples, "metadata",
"metadata.xlsx")
if os.path.exists(metadata_file):
temp = pd.read_excel(metadata_file)
meta_attrs = temp.columns.values
metadata = temp.values
with self.output().temporary_path() as out_file:
attrs = {"title": self.tissue}
valid_cells = []
sample_files = [s.fn for s in self.input()]
for sample in sorted(sample_files):
# Connect and perform file-specific cell validation
with loompy.connect(sample) as ds:
logging.info("Marking invalid cells")
(mols, genes) = ds.map([np.sum, np.count_nonzero], axis=1)
valid_cells.append(
np.logical_and(mols >= 600,
(mols / genes) >= 1.2).astype('int'))
ds.ca.Total = mols
ds.ca.NGenes = genes
logging.info("Computing mito/ribo ratio for " + sample)
mito = np.where(npstr.startswith(ds.ra.Gene, "mt-"))[0]
ribo = np.where(npstr.startswith(ds.ra.Gene, "Rpl"))[0]
ribo = np.union1d(
ribo,
np.where(npstr.startswith(ds.ra.Gene, "Rps"))[0])
if len(ribo) > 0 and len(mito) > 0:
mitox = ds[mito, :]
ribox = ds[ribo, :]
ratio = (mitox.sum(axis=0) + 1) / (ribox.sum(axis=0) +
1)
ds.ca.MitoRiboRatio = ratio
logging.info("Creating combined loom file")
loompy.combine(sample_files,
out_file,
key="Accession",
file_attrs=attrs)
# Validating genes
logging.info("Marking invalid genes")
with loompy.connect(out_file) as ds:
vgpath = os.path.join(am.paths().build, "genes.txt")
if os.path.exists(vgpath):
valids = np.zeros(ds.shape[0])
with open(vgpath, "r") as f:
line = f.readline()
items = line[:-1].split("\t")
valids[np.where(ds.Accession == items[0])] = int(
items[1])
ds.set_attr("_Valids", valids, axis=0)
else:
nnz = ds.map([np.count_nonzero], axis=0)[0]
valid_genes = np.logical_and(nnz > 10,
nnz < ds.shape[1] * 0.6)
ds.set_attr("_Valid", valid_genes, axis=0)
logging.info("Marking invalid cells")
ds.set_attr("_Valid", np.concatenate(valid_cells), axis=1)
n_valid = np.sum(ds.col_attrs["_Valid"] == 1)
n_total = ds.shape[1]
logging.info("%d of %d cells were valid", n_valid, n_total)
classifier_path = os.path.join(am.paths().samples,
"classified",
"classifier.pickle")
if os.path.exists(classifier_path):
logging.info("Classifying cells by major class")
with open(classifier_path, "rb") as f:
clf = pickle.load(f) # type: cg.Classifier
np.random.seed(13)
(classes, probs,
class_labels) = clf.predict(ds, probability=True)
mapping = {
"Astrocyte": "Astrocytes",
"Astrocyte,Cycling": "Astrocytes",
"Astrocyte,Immune": None,
"Astrocyte,Neurons": None,
"Astrocyte,Oligos": None,
"Astrocyte,Vascular": None,
"Bergmann-glia": "Astrocytes",
"Blood": "Blood",
"Blood,Cycling": "Blood",
"Blood,Vascular": None,
"Enteric-glia": "PeripheralGlia",
"Enteric-glia,Cycling": "PeripheralGlia",
"Ependymal": "Ependymal",
"Ex-Astrocyte": None,
"Ex-Blood": None,
"Ex-Immune": None,
"Ex-Neurons": None,
"Ex-Oligos": None,
"Ex-Vascular": None,
"Immune": "Immune",
"Immune,Neurons": None,
"Immune,Oligos": None,
"Neurons": "Neurons",
"Neurons,Cycling": "Neurons",
"Neurons,Immune": None,
"Neurons,Oligos": None,
"Neurons,Satellite-glia": None,
"OEC": "Astrocytes",
"Oligos": "Oligos",
"Oligos,Cycling": "Oligos",
"Oligos,Immune": None,
"Oligos,Vascular": None,
"Satellite-glia": "PeripheralGlia",
"Satellite-glia,Cycling": "PeripheralGlia",
"Schwann": "PeripheralGlia",
"Schwann,Cycling": "PeripheralGlia",
"Satellite-glia,Schwann": None,
"Ttr": "Ependymal",
"Vascular": "Vascular",
"Vascular,Cycling": "Vascular",
"Neurons,Vascular": None,
"Vascular,Oligos": None,
"Satellite-glia,Vascular": None,
"Unknown": None,
"Outliers": None
}
classes_pooled = np.array(
[str(mapping[c]) for c in classes], dtype=np.object_)
# mask invalid cells
classes[ds.col_attrs["_Valid"] == 0] = "Excluded"
classes_pooled[ds.col_attrs["_Valid"] == 0] = "Excluded"
classes_pooled[classes_pooled == "None"] = "Excluded"
ds.set_attr("Class", classes_pooled.astype('str'), axis=1)
ds.set_attr("Subclass", classes.astype('str'), axis=1)
for ix, cls in enumerate(class_labels):
ds.set_attr("ClassProbability_" + str(cls),
probs[:, ix],
axis=1)
else:
logging.info(
"No classifier found in this build directory - skipping."
)
ds.set_attr("Class",
np.array(["Unknown"] * ds.shape[1]),
axis=1)
ds.set_attr("Subclass",
np.array(["Unknown"] * ds.shape[1]),
axis=1)
def formula(menage, period):
depcom = menage('depcom', period)
return sum([
startswith(depcom, code_departement)
for code_departement in DEPARTEMENTS_OCCITANIE
]) > 0
def function(self, simulation, period):
depcom = simulation.calculate('depcom', period)
return period, startswith(depcom, '972')
def _setup_spec_cube(self):
self.spec_cube = True
self.geometry = "spectral_cube"
end = min(self.dimensionality+1,4)
if self.events_data:
ctypes = self.axis_names
else:
ctypes = np.array([self.primary_header["CTYPE%d" % (i)]
for i in range(1,end)])
log_str = "Detected these axes: "+"%s "*len(ctypes)
mylog.info(log_str % tuple([ctype for ctype in ctypes]))
self.lat_axis = np.zeros((end-1), dtype="bool")
for p in lat_prefixes:
self.lat_axis += np_char.startswith(ctypes, p)
self.lat_axis = np.where(self.lat_axis)[0][0]
self.lat_name = ctypes[self.lat_axis].split("-")[0].lower()
self.lon_axis = np.zeros((end-1), dtype="bool")
for p in lon_prefixes:
self.lon_axis += np_char.startswith(ctypes, p)
self.lon_axis = np.where(self.lon_axis)[0][0]
self.lon_name = ctypes[self.lon_axis].split("-")[0].lower()
if self.lat_axis == self.lon_axis and self.lat_name == self.lon_name:
self.lat_axis = 1
self.lon_axis = 0
self.lat_name = "Y"
self.lon_name = "X"
if self.wcs.naxis > 2:
self.spec_axis = np.zeros((end-1), dtype="bool")
for p in spec_names.keys():
self.spec_axis += np_char.startswith(ctypes, p)
self.spec_axis = np.where(self.spec_axis)[0][0]
self.spec_name = spec_names[ctypes[self.spec_axis].split("-")[0][0]]
self.wcs_2d = _astropy.pywcs.WCS(naxis=2)
self.wcs_2d.wcs.crpix = self.wcs.wcs.crpix[[self.lon_axis, self.lat_axis]]
self.wcs_2d.wcs.cdelt = self.wcs.wcs.cdelt[[self.lon_axis, self.lat_axis]]
self.wcs_2d.wcs.crval = self.wcs.wcs.crval[[self.lon_axis, self.lat_axis]]
self.wcs_2d.wcs.cunit = [str(self.wcs.wcs.cunit[self.lon_axis]),
str(self.wcs.wcs.cunit[self.lat_axis])]
self.wcs_2d.wcs.ctype = [self.wcs.wcs.ctype[self.lon_axis],
self.wcs.wcs.ctype[self.lat_axis]]
self._p0 = self.wcs.wcs.crpix[self.spec_axis]
self._dz = self.wcs.wcs.cdelt[self.spec_axis]
self._z0 = self.wcs.wcs.crval[self.spec_axis]
self.spec_unit = str(self.wcs.wcs.cunit[self.spec_axis])
if self.spectral_factor == "auto":
self.spectral_factor = float(max(self.domain_dimensions[[self.lon_axis,
self.lat_axis]]))
self.spectral_factor /= self.domain_dimensions[self.spec_axis]
mylog.info("Setting the spectral factor to %f" % (self.spectral_factor))
Dz = self.domain_right_edge[self.spec_axis]-self.domain_left_edge[self.spec_axis]
self.domain_right_edge[self.spec_axis] = self.domain_left_edge[self.spec_axis] + \
self.spectral_factor*Dz
self._dz /= self.spectral_factor
self._p0 = (self._p0-0.5)*self.spectral_factor + 0.5
else:
self.wcs_2d = self.wcs
self.spec_axis = 2
self.spec_name = "z"
self.spec_unit = "code_length"
def formula(self, simulation, period):
depcom = simulation.calculate('depcom', period)
return startswith(depcom, '971')
def function(self, simulation, period):
period = period.start.period('year').offset('first-of')
depcom = simulation.calculate('depcom', period)
return period, np.logical_or(startswith(depcom, '97'),
startswith(depcom, '98'))
# Chapter 13 颜色空间转换
import cv2
from numpy.core.defchararray import startswith
import numpy as np
# 13.1 转换颜色空间
flag = 0
for i in dir(cv2):
if startswith(i, 'COLOR_'):
flag += 1
print(flag) # 共有 274 种 cv2.COLOR_xxx
# 13.2 物体跟踪
def FindBlue(): # 识别视频中的蓝色物体并跟踪显示
cap = cv2.VideoCapture(0)
while cap.isOpened():
# 获取每一帧
ret, frame = cap.read()
# 转换到 HSV
hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV)
# 设定蓝色的阈值
lower_blue = np.array([100, 43, 46])
upper_blue = np.array([124, 255, 255])
# 根据阈值构建 mask
mask = cv2.inRange(hsv, lower_blue, upper_blue)
# 对原图像和 mask 进行位运算
res = cv2.bitwise_and(frame, frame, mask=mask)
# 显示图片
cv2.imshow('src', res)
def _parse_parameter_file(self):
if self.parameter_filename.startswith("InMemory"):
self.unique_identifier = time.time()
else:
self.unique_identifier = \
int(os.stat(self.parameter_filename)[stat.ST_CTIME])
# Determine dimensionality
self.dimensionality = self.naxis
self.geometry = "cartesian"
# Sometimes a FITS file has a 4D datacube, in which case
# we take the 4th axis and assume it consists of different fields.
if self.dimensionality == 4: self.dimensionality = 3
self.domain_dimensions = np.array(self.dims)[:self.dimensionality]
if self.dimensionality == 2:
self.domain_dimensions = np.append(self.domain_dimensions,
[int(1)])
self.domain_left_edge = np.array([0.5]*3)
self.domain_right_edge = np.array([float(dim)+0.5 for dim in self.domain_dimensions])
if self.dimensionality == 2:
self.domain_left_edge[-1] = 0.5
self.domain_right_edge[-1] = 1.5
# Get the simulation time
try:
self.current_time = self.parameters["time"]
except:
mylog.warning("Cannot find time")
self.current_time = 0.0
pass
# For now we'll ignore these
self.periodicity = (False,)*3
self.current_redshift = self.omega_lambda = self.omega_matter = \
self.hubble_constant = self.cosmological_simulation = 0.0
if self.dimensionality == 2 and self.z_axis_decomp:
mylog.warning("You asked to decompose along the z-axis, but this is a 2D dataset. " +
"Ignoring.")
self.z_axis_decomp = False
if self.events_data: self.specified_parameters["nprocs"] = 1
# If nprocs is None, do some automatic decomposition of the domain
if self.specified_parameters["nprocs"] is None:
if self.z_axis_decomp:
nprocs = np.around(self.domain_dimensions[2]/8).astype("int")
else:
nprocs = np.around(np.prod(self.domain_dimensions)/32**self.dimensionality).astype("int")
self.parameters["nprocs"] = max(min(nprocs, 512), 1)
else:
self.parameters["nprocs"] = self.specified_parameters["nprocs"]
# Check to see if this data is in some kind of (Lat,Lon,Vel) format
self.spec_cube = False
self.wcs_2d = None
x = 0
for p in lon_prefixes+lat_prefixes+list(spec_names.keys()):
y = np_char.startswith(self.axis_names[:self.dimensionality], p)
x += np.any(y)
if x == self.dimensionality:
if self.axis_names == ['LINEAR','LINEAR']:
self.wcs_2d = self.wcs
self.lat_axis = 1
self.lon_axis = 0
self.lat_name = "Y"
self.lon_name = "X"
else:
self._setup_spec_cube()