def getSample(self):
'''gets a sample trajectory from
the specified domain
'''
d = Chain()
if self.domain == "blackjack":
d = Game()
elif self.domain == "wumpus":
d = Grid(4)
elif self.domain == "blocksworld":
d = BW(4)
elif self.domain == "traffic":
d = TrafficSignal()
elif self.domain == "pong":
d = Pong()
elif self.domain == "tetris":
d = Tetris()
#elif wumpus
sample = []
state = d
actions = d.actions
while True:
if state == "winner" or state == "loser":
sample += [deepcopy(state)]
break
sample += [deepcopy(str(state))]
action = actions[randint(0,len(actions)-1)]
state = d.takeAction(state,action)
return sample
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain = self.model[chain_id]
warnings.warn(
"WARNING: Chain %s is discontinuous at line %i." %
(chain_id, self.line_counter), PDBConstructionWarning)
else:
self.chain = Chain(chain_id)
self.model.add(self.chain)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain = self.model[chain_id]
if __debug__:
sys.stderr.write(
"WARNING: Chain %s is discontinuous at line %i.\n" %
(chain_id, self.line_counter))
else:
self.chain = Chain(chain_id)
self.model.add(self.chain)
def __init__(self,FA="LSReg",domain="50chain",N=100,loss="ls",trees=500,type="max",depth=2):
'''class constructor'''
self.domain = domain
if domain == "50chain":
self.domObj = Chain()
elif domain == "blackjack":
self.domObj = Game()
elif domain == "wumpus":
self.domObj = Grid(4)
elif domain == "blocksworld":
self.domObj = BW(4)
elif domain == "traffic":
self.domObj = TrafficSignal()
elif domain == "pong":
self.domObj = Pong()
elif domain == "tetris":
self.domObj = Tetris()
if FA == "LSReg":
self.FA = LSReg()
elif FA == "NN":
self.FA = NeuralNetwork()
elif FA == "GB":
self.FA = GradientBooster(loss=loss,trees=trees,depth=depth)
self.value,self.count = {},{}
self.values = [{} for i in range(N)]
self.approxValues = [{} for i in range(N)]
self.BE = []
self.type = type
self.TD(self.FA,N)
def __init__(self, spec):
Chain.__init__(self)
assert (spec["Type"] == "MultiLevel")
self.ChainSpec = spec["Chain"]
self.Licenses = spec["Licenses"]
for lic in self.Licenses:
lic["Count"] = lic["MaxCount"]
self.Tasks = {}
for i, taskSpec in enumerate(spec["Tasks"]):
if self.FindTaskInChain(taskSpec["Name"]) == None:
print "MultiLevelChain: Task %s not referenced in the chain, skipping it" % taskSpec[
"Name"]
continue
task = Tasks.Create(self, taskSpec)
task.ID = i + 1
self.Tasks[task.Name] = task
Chain.Initialize(self)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain=self.model[chain_id]
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
% (chain_id, self.line_counter),
PDBConstructionWarning)
else:
self.chain=Chain(chain_id)
self.model.add(self.chain)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain=self.model[chain_id]
if __debug__:
sys.stderr.write("WARNING: Chain %s is discontinuous at line %i.\n"
% (chain_id, self.line_counter))
else:
self.chain=Chain(chain_id)
self.model.add(self.chain)
def build_chains(self):
chains = {}
for residue in self.residues:
if residue.chain_id not in chains:
chains[residue.chain_id] = Chain(residue.chain_id)
for residue in self.residues:
chains[residue.chain_id].residues.append(residue)
chainlist = []
for chain in chains.values():
chainlist.append(chain.chain_id)
print("Found ", len(chains.values()), " chains: ", chainlist)
print("\n")
return chains.values()
def processSingleRunChain(args=None):
'''
Function to run single runChain object
Setup the run chain object with the args
'''
e_handler = EventsHandler()
runchain = Chain(e_handler)
e_handler.addObserver(runchain)
run_num = None
for k in args['rundetails'].keys():
run_num = k
#print 'process is ', mp.current_process().name , ' for run ', run_num
runchain.commands = args['commands']
#print 'commands', runchain.commands
rfolder = args['result_folder']
initialEvent = SimpleEvent('init', True, {'run':run_num, 'result_folder':rfolder})
runchain.startChainWithEvent(initialEvent)
return runchain.getResult()
def test():
from Connectable import Connectable
class A(Connectable):
sockets = {
'out': ['1'],
}
def _update(self):
self._outputs['1'] = 1
return
pass
a = A()
from Passer import Passer
class B(Passer):
sockets = {
'in': ['1'],
'out': ['1'],
}
pass
b = B()
class C(Connectable):
sockets = {
'in': ['in3'],
'out': ['out'],
}
def _update(self):
self._outputs['out'] = self._inputs['in3']
return
pass
c = C()
from Node import Node
n1 = Node( None, a, '1' )
n2 = Node( '1', b, '1' )
n3 = Node( 'in3', c, None )
from Chain import Chain
ch = Chain()
ch.append( n1 )
ch.append( n2 )
ch.append( n3 )
from Chains import Chains
cs = Chains()
cs.add( ch )
r = Runner()
r( cs )
assert c.getOutput( 'out' ) == 1
return
def copy(self, db):
# Copy chains list
self.chains = np.array([Chain(-1)] * db.num_edges)
for i in range(0, len(db.chains)):
self.chains[i].copy(db.chains[i])
# Copy edges list
self.edges = deepcopy(db.edges)
# Copy nodes list
self.nodes = deepcopy(db.nodes)
self.num_edges = db.num_edges
self.rows = db.rows
self.columns = db.columns
self.score1 = db.score1
self.score2 = db.score2
self.curr_player = db.curr_player
def chain_builder(nouns):
chains = {}
word_dict = {}
for noun in nouns:
if noun not in word_dict.keys():
word_dict[noun] = 1
is_new_chain = True
for chain_key in chains.keys():
if noun in chains[chain_key].syn_list or noun in chains[chain_key].anto_list or noun in chains[chain_key].hypo_list or noun in chains[chain_key].hyper_list:
chains[chain_key].add_word_to_lexical_chain(noun)
is_new_chain = False
break
if is_new_chain:
syn_list, anto_list, hypo_list, hyper_list = get_relationships(noun)
chains[noun] = Chain(noun, syn_list, anto_list, hypo_list, hyper_list)
else:
word_dict[noun] += 1
return chains, word_dict
import os
import sys
sys.path.append("../src")
from Chain import Chain
from Likelihood_Planck import Likelihood_Planck
# Prepare the likelihoods
likelihoods = ["commander", "CAMspec", "lowlike"]
clik_dir = "/home/torradocacho/codes/stable/planck_likelihood_1303"
lik = Likelihood_Planck(base_folder=clik_dir, likelihoods=likelihoods)
# Prepare the spectra
CHAINS = "/data/misc/torradocacho/chains"
base_folder = os.path.join(CHAINS, "historicas/aaot/gaussN/07_final")
chain = Chain(os.path.join(base_folder, "gaussN_var_c"))
# 2 best fits
best_fit_points = chain.best_fit(how_many=2)
class_folder = "/home/torradocacho/cosmo/code/class_v1.7.2_external_Pk"
# Overall best fit
best_fit_point = best_fit_points[1]
override_params = {
"command":
"python " +
os.path.join(class_folder, "external_Pk/generate_Pk_from_u_gaussN.py")
}
spectrum_bf1 = chain.CMBspectrum_from_point(best_fit_point,
class_folder=class_folder,
override_params=override_params,
import os
import sys
sys.path.append("../src")
from Chain import Chain
from plot_Cl_CMB import plot_Cl_CMB
base_folder = "./chains"
name = "planck_WP"
chain = Chain(os.path.join(base_folder, name))
class_folder = "/home/torradocacho/cosmo/code/class_v1.7.2"
spectrum = chain.CMBspectrum_from_point(chain.best_fit(),
class_folder=class_folder,
verbose=True)
plot_Cl_CMB([spectrum], title="Best fit CMB spectrum")
class StructureBuilder:
"""
Deals with contructing the Structure object. The StructureBuilder class is used
by the PDBParser classes to translate a file to a Structure object.
"""
def __init__(self):
self.line_counter = 0
self.header = {}
def _is_completely_disordered(self, residue):
"Return 1 if all atoms in the residue have a non blanc altloc."
atom_list = residue.get_unpacked_list()
for atom in atom_list:
altloc = atom.get_altloc()
if altloc == " ":
return 0
return 1
# Public methods called by the Parser classes
def set_header(self, header):
self.header = header
def set_line_counter(self, line_counter):
"""
The line counter keeps track of the line in the PDB file that
is being parsed.
Arguments:
o line_counter - int
"""
self.line_counter = line_counter
def init_structure(self, structure_id):
"""Initiate a new Structure object with given id.
Arguments:
o id - string
"""
self.structure = Structure(structure_id)
def init_model(self, model_id):
"""Initiate a new Model object with given id.
Arguments:
o id - int
"""
self.model = Model(model_id)
self.structure.add(self.model)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain = self.model[chain_id]
if __debug__:
sys.stderr.write(
"WARNING: Chain %s is discontinuous at line %i.\n" %
(chain_id, self.line_counter))
else:
self.chain = Chain(chain_id)
self.model.add(self.chain)
def init_seg(self, segid):
"""Flag a change in segid.
Arguments:
o segid - string
"""
self.segid = segid
def init_residue(self, resname, field, resseq, icode):
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blanc.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if field != " ":
if field == "H":
# The hetero field consists of H_ + the residue name (e.g. H_FUC)
field = "H_" + resname
res_id = (field, resseq, icode)
if field == " ":
if self.chain.has_id(res_id):
# There already is a residue with the id (field, resseq, icode).
# This only makes sense in the case of a point mutation.
if __debug__:
sys.stderr.write(
"WARNING: Residue ('%s', %i, '%s') redefined at line %i.\n"
% (field, resseq, icode, self.line_counter))
duplicate_residue = self.chain[res_id]
if duplicate_residue.is_disordered() == 2:
# The residue in the chain is a DisorderedResidue object.
# So just add the last Residue object.
if duplicate_residue.disordered_has_id(resname):
# The residue was already made
self.residue = duplicate_residue
duplicate_residue.disordered_select(resname)
else:
# Make a new residue and add it to the already
# present DisorderedResidue
new_residue = Residue(res_id, resname, self.segid)
duplicate_residue.disordered_add(new_residue)
self.residue = duplicate_residue
return
else:
# Make a new DisorderedResidue object and put all
# the Residue objects with the id (field, resseq, icode) in it.
# These residues each should have non-blanc altlocs for all their atoms.
# If not, the PDB file probably contains an error.
if not self._is_completely_disordered(duplicate_residue):
# if this exception is ignored, a residue will be missing
self.residue = None
raise PDBConstructionException(\
"Blank altlocs in duplicate residue %s ('%s', %i, '%s')" \
% (resname, field, resseq, icode))
self.chain.detach_child(res_id)
new_residue = Residue(res_id, resname, self.segid)
disordered_residue = DisorderedResidue(res_id)
self.chain.add(disordered_residue)
disordered_residue.disordered_add(duplicate_residue)
disordered_residue.disordered_add(new_residue)
self.residue = disordered_residue
return
residue = Residue(res_id, resname, self.segid)
self.chain.add(residue)
self.residue = residue
def init_atom(self,
name,
coord,
b_factor,
occupancy,
altloc,
fullname,
serial_number=None):
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
"""
residue = self.residue
# if residue is None, an exception was generated during
# the construction of the residue
if residue is None:
return
# First check if this atom is already present in the residue.
# If it is, it might be due to the fact that the two atoms have atom
# names that differ only in spaces (e.g. "CA.." and ".CA.",
# where the dots are spaces). If that is so, use all spaces
# in the atom name of the current atom.
if residue.has_id(name):
duplicate_atom = residue[name]
# atom name with spaces of duplicate atom
duplicate_fullname = duplicate_atom.get_fullname()
if duplicate_fullname != fullname:
# name of current atom now includes spaces
name = fullname
if __debug__:
sys.stderr.write(
"WARNING: atom names %s and %s differ only in spaces at line %i.\n"
% (duplicate_fullname, fullname, self.line_counter))
atom = self.atom = Atom(name, coord, b_factor, occupancy, altloc,
fullname, serial_number)
if altloc != " ":
# The atom is disordered
if residue.has_id(name):
# Residue already contains this atom
duplicate_atom = residue[name]
if duplicate_atom.is_disordered() == 2:
duplicate_atom.disordered_add(atom)
else:
# This is an error in the PDB file:
# a disordered atom is found with a blanc altloc
# Detach the duplicate atom, and put it in a
# DisorderedAtom object together with the current
# atom.
residue.detach_child(name)
disordered_atom = DisorderedAtom(name)
residue.add(disordered_atom)
disordered_atom.disordered_add(atom)
disordered_atom.disordered_add(duplicate_atom)
residue.flag_disordered()
if __debug__:
sys.stderr.write(
"WARNING: disordered atom found with blanc altloc before line %i.\n"
% self.line_counter)
else:
# The residue does not contain this disordered atom
# so we create a new one.
disordered_atom = DisorderedAtom(name)
residue.add(disordered_atom)
# Add the real atom to the disordered atom, and the
# disordered atom to the residue
disordered_atom.disordered_add(atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add(atom)
def set_anisou(self, anisou_array):
"Set anisotropic B factor of current Atom."
self.atom.set_anisou(anisou_array)
def set_siguij(self, siguij_array):
"Set standard deviation of anisotropic B factor of current Atom."
self.atom.set_siguij(siguij_array)
def set_sigatm(self, sigatm_array):
"Set standard deviation of atom position of current Atom."
self.atom.set_sigatm(sigatm_array)
def get_structure(self):
"Return the structure."
# first sort everything
# self.structure.sort()
# Add the header dict
self.structure.header = self.header
return self.structure
def set_symmetry(self, spacegroup, cell):
pass
from Chain import Chain
from flask import Flask, render_template, request
app = Flask(__name__)
my_chain = Chain()
@app.route("/")
@app.route("/home")
def home():
return render_template("home.html", blocks=my_chain.block_chain)
#to add a transaction "/add?tx=some-transaction"
@app.route("/add")
def add():
query = request.args.get('tx')
my_chain.add_data(query)
return render_template("add.html", query=query, message="query added")
@app.route("/mine")
def mine():
message = my_chain.create_block()
return render_template("mine.html", message=message)
if __name__ == '__main__':
app.run(debug=True)
import os
import sys
sys.path.append("../src")
from Chain import Chain
from plot_Cl_CMB import plot_Cl_CMB
base_folder = "./chains"
name = "planck_WP"
chain = Chain(os.path.join(base_folder, name))
class_folder = "/home/torradocacho/cosmo/code/class_v1.7.2"
spectrum = chain.CMBspectrum_from_point(chain.best_fit(),
class_folder=class_folder,
verbose=True)
plot_Cl_CMB([spectrum], title = "Best fit CMB spectrum")
def chain():
from Chain import Chain
return Chain()
import os
import sys
sys.path.append("../src")
from Chain import Chain
from plot_lik import plot_lik_2D
base_folder = "./chains"
chain_name = "planck_WP"
chain = Chain(os.path.join(base_folder, chain_name))
labels = {"omega_b": r"$\omega_\mathrm{B}$",
"omega_cdm": r"$\omega_\mathrm{C}$",
"H0": r"$H_0$",
"tau_reio": r"$\tau_\mathrm{reio}$",
"A_s": r"$A_s$",
"n_s": r"$n_s$",}
chain.set_parameter_labels(labels)
chain.plot_correlation(params = labels.keys(), save_file="correlations.png")
class StructureBuilder:
"""
Deals with contructing the Structure object. The StructureBuilder class is used
by the PDBParser classes to translate a file to a Structure object.
"""
def __init__(self):
self.line_counter=0
self.header={}
def _is_completely_disordered(self, residue):
"Return 1 if all atoms in the residue have a non blank altloc."
atom_list=residue.get_unpacked_list()
for atom in atom_list:
altloc=atom.get_altloc()
if altloc==" ":
return 0
return 1
# Public methods called by the Parser classes
def set_header(self, header):
self.header=header
def set_line_counter(self, line_counter):
"""
The line counter keeps track of the line in the PDB file that
is being parsed.
Arguments:
o line_counter - int
"""
self.line_counter=line_counter
def init_structure(self, structure_id):
"""Initiate a new Structure object with given id.
Arguments:
o id - string
"""
self.structure=Structure(structure_id)
def init_model(self, model_id):
"""Initiate a new Model object with given id.
Arguments:
o id - int
"""
self.model=Model(model_id)
self.structure.add(self.model)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain=self.model[chain_id]
if __debug__:
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
% (chain_id, self.line_counter),
PDBConstructionWarning)
else:
self.chain=Chain(chain_id)
self.model.add(self.chain)
def init_seg(self, segid):
"""Flag a change in segid.
Arguments:
o segid - string
"""
self.segid=segid
def init_residue(self, resname, field, resseq, icode):
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if field!=" ":
if field=="H":
# The hetero field consists of H_ + the residue name (e.g. H_FUC)
field="H_"+resname
res_id=(field, resseq, icode)
if field==" ":
if self.chain.has_id(res_id):
# There already is a residue with the id (field, resseq, icode).
# This only makes sense in the case of a point mutation.
if __debug__:
warnings.warn("WARNING: Residue ('%s', %i, '%s') "
"redefined at line %i."
% (field, resseq, icode, self.line_counter),
PDBConstructionWarning)
duplicate_residue=self.chain[res_id]
if duplicate_residue.is_disordered()==2:
# The residue in the chain is a DisorderedResidue object.
# So just add the last Residue object.
if duplicate_residue.disordered_has_id(resname):
# The residue was already made
self.residue=duplicate_residue
duplicate_residue.disordered_select(resname)
else:
# Make a new residue and add it to the already
# present DisorderedResidue
new_residue=Residue(res_id, resname, self.segid)
duplicate_residue.disordered_add(new_residue)
self.residue=duplicate_residue
return
else:
# Make a new DisorderedResidue object and put all
# the Residue objects with the id (field, resseq, icode) in it.
# These residues each should have non-blank altlocs for all their atoms.
# If not, the PDB file probably contains an error.
if not self._is_completely_disordered(duplicate_residue):
# if this exception is ignored, a residue will be missing
self.residue=None
raise PDBConstructionException(\
"Blank altlocs in duplicate residue %s ('%s', %i, '%s')" \
% (resname, field, resseq, icode))
self.chain.detach_child(res_id)
new_residue=Residue(res_id, resname, self.segid)
disordered_residue=DisorderedResidue(res_id)
self.chain.add(disordered_residue)
disordered_residue.disordered_add(duplicate_residue)
disordered_residue.disordered_add(new_residue)
self.residue=disordered_residue
return
residue=Residue(res_id, resname, self.segid)
self.chain.add(residue)
self.residue=residue
def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname,
serial_number=None, element=None):
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
o element - string, upper case, e.g. "HG" for mercury
"""
residue=self.residue
# if residue is None, an exception was generated during
# the construction of the residue
if residue is None:
return
# First check if this atom is already present in the residue.
# If it is, it might be due to the fact that the two atoms have atom
# names that differ only in spaces (e.g. "CA.." and ".CA.",
# where the dots are spaces). If that is so, use all spaces
# in the atom name of the current atom.
if residue.has_id(name):
duplicate_atom=residue[name]
# atom name with spaces of duplicate atom
duplicate_fullname=duplicate_atom.get_fullname()
if duplicate_fullname!=fullname:
# name of current atom now includes spaces
name=fullname
if __debug__:
warnings.warn("WARNING: atom names %s and %s differ "
"only in spaces at line %i."
% (duplicate_fullname, fullname,
self.line_counter),
PDBConstructionWarning)
atom=self.atom=Atom(name, coord, b_factor, occupancy, altloc,
fullname, serial_number, element)
if altloc!=" ":
# The atom is disordered
if residue.has_id(name):
# Residue already contains this atom
duplicate_atom=residue[name]
if duplicate_atom.is_disordered()==2:
duplicate_atom.disordered_add(atom)
else:
# This is an error in the PDB file:
# a disordered atom is found with a blank altloc
# Detach the duplicate atom, and put it in a
# DisorderedAtom object together with the current
# atom.
residue.detach_child(name)
disordered_atom=DisorderedAtom(name)
residue.add(disordered_atom)
disordered_atom.disordered_add(atom)
disordered_atom.disordered_add(duplicate_atom)
residue.flag_disordered()
if __debug__:
warnings.warn("WARNING: disordered atom found "
"with blank altloc before line %i.\n"
% self.line_counter,
PDBConstructionWarning)
else:
# The residue does not contain this disordered atom
# so we create a new one.
disordered_atom=DisorderedAtom(name)
residue.add(disordered_atom)
# Add the real atom to the disordered atom, and the
# disordered atom to the residue
disordered_atom.disordered_add(atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add(atom)
def set_anisou(self, anisou_array):
"Set anisotropic B factor of current Atom."
self.atom.set_anisou(anisou_array)
def set_siguij(self, siguij_array):
"Set standard deviation of anisotropic B factor of current Atom."
self.atom.set_siguij(siguij_array)
def set_sigatm(self, sigatm_array):
"Set standard deviation of atom position of current Atom."
self.atom.set_sigatm(sigatm_array)
def get_structure(self):
"Return the structure."
# first sort everything
# self.structure.sort()
# Add the header dict
self.structure.header=self.header
return self.structure
def set_symmetry(self, spacegroup, cell):
pass
backgroundFilesBatched.append(
backgroundFiles[((2 * i + 1) * args.numberOfBatches - b) %
len(backgroundFiles)][0])
batchStartBackground = int(
round(1. * len(backgroundFilesBatched) / args.numberOfBatches *
args.currentBatchNumber))
batchEndBackground = int(
round(1. * len(backgroundFilesBatched) / args.numberOfBatches *
(args.currentBatchNumber + 1)))
print "bkg slice: ", batchStartBackground, "-", batchEndBackground, "/", len(
backgroundFilesBatched)
#sys.exit(1)
#signalFiles = signalFiles[:10]
signalChain = Chain(map(lambda f: f[0], signalFiles))
backgroundChain = Chain(
backgroundFilesBatched[batchStartBackground:batchEndBackground])
#backgroundChain = Chain([backgroundFiles[0][0]])#,backgroundFiles[1][0]])
convert(
args.output,
signalChain,
backgroundChain,
repeatSignal=args.repeatSignal,
nBatch=args.numberOfBatches,
batch=args.currentBatchNumber,
maxCombinations=20,
maxGenIndex=20,
)
elif choice == 2:
os.system('clear')
print(color['BLUE'] + "[PyBlock:NewChain]" + color['ENDC'])
print()
print(color['LGREEN'] + "1." + color['ENDC'] + "New")
print(color['LGREEN'] + "2." + color['ENDC'] +
"Copy From Previous Chain")
print(color['LRED'] + "0." + color['ENDC'] + "Exit")
print()
c = int(input(color['LGREEN'] + ">" + color['ENDC']))
if c == 0:
continue
if c == 1:
name = input("Chain Name" + color['LGREEN'] + ">" +
color['ENDC'])
chains.append(Chain(name))
print(color['GREEN'] + "New Chain Added" + color['ENDC'])
save()
if c == 2:
idx = int(
input("Chain Index" + color['LGREEN'] + ">" +
color['ENDC']))
name = input("Chain Name" + color['LGREEN'] + ">" +
color['ENDC'])
try:
c = chains[idx - 1].fork()
c.name = name
chains.append(c)
print(color['GREEN'] + "New Chain Added" +
color['ENDC'])
save()
import threading, json, time from Broadcast import Broadcast import Broadcast as bd from Chain import Chain, get_lock, release_lock from chain_utils import get_blocks, append_block # from Transaction import Broadcast.txnBuffer from Block import block_size, Block CH = Chain() BR = Broadcast() # broadcast reciever t1 = threading.Thread(target = BR.recieve_broadcast) # tcp data reciever t2 = threading.Thread(target = BR.recieve_data) # im alive broadcast t3 = threading.Thread(target = BR.imAlive) # im alive broadcast t4 = threading.Thread(target = BR.shareChain) t1.start() t2.start() t3.start() t4.start() while True:
def compute_transfer_model(self):
X,Y,bk = [],[],[]
i = 0
values = {}
while i < self.transfer+1: #at least one iteration burn in time
if self.simulator == "logistics":
state = Logistics(number = self.state_number,start=True)
if not bk:
bk = Logistics.bk
elif self.simulator == "pong":
state = Pong(number = self.state_number,start=True)
if not bk:
bk = Pong.bk
elif self.simulator == "tetris":
state = Tetris(number = self.state_number,start=True)
if not bk:
bk = Tetris.bk
elif self.simulator == "wumpus":
state = Wumpus(number = self.state_number,start=True)
if not bk:
bk = Wumpus.bk
elif self.simulator == "blocks":
state = Blocks_world(number = self.state_number,start=True)
if not bk:
bk = Blocks_world.bk
elif self.simulator == "blackjack":
state = Game(number = self.state_number,start=True)
if not bk:
bk = Game.bk
elif self.simulator == "50chain":
state = Chain(number = self.state_number,start=True)
if not bk:
bk = Chain.bk
elif self.simulator == "net_admin":
state = Admin(number = self.state_number,start=True)
if not bk:
bk = Admin.bk
with open(self.simulator+"_transfer_out.txt","a") as f:
if self.transfer:
f.write("start state: "+str(state.get_state_facts())+"\n")
time_elapsed = 0
within_time = True
start = clock()
trajectory = [(state.state_number,state.get_state_facts())]
while not state.goal():
if self.transfer:
f.write("="*80+"\n")
state_action_pair = state.execute_random_action()
state = state_action_pair[0] #state
if self.transfer:
f.write(str(state.get_state_facts())+"\n")
trajectory.append((state.state_number,state.get_state_facts()))
end = clock()
time_elapsed = abs(end-start)
if self.simulator == "logistics" and time_elapsed > 0.5:
within_time = False
break
elif self.simulator == "pong" and time_elapsed > 1000:
within_time = False
break
elif self.simulator == "tetris" and time_elapsed > 1000:
within_time = False
break
elif self.simulator == "wumpus" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "blocks" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "blackjack" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "50chain" and time_elapsed > 2:
within_time = False
break
elif self.simulator == "net_admin" and time_elapsed > 1:
within_time = False
break
if within_time:
self.compute_value_of_trajectory(values,trajectory)
self.state_number += len(trajectory)+1
for key in values:
state = list(key[1])
value = values[key]
X.append(state)
Y.append(value)
'''
for key in values:
facts += list(key[1])
example_predicate = "value(s"+str(key[0])+") "+str(values[key])
examples.append(example_predicate)
'''
i += 1
npX = np.array(X)
npY = np.array(Y)
if not self.transfer:
npY = np.zeros(len(npY))
model = MLPRegressor(hidden_layer_sizes=(25,),
activation="logistic",
solver="lbfgs",
alpha=0.0001,
batch_size="auto",
learning_rate="constant",
learning_rate_init=0.001,
power_t=0.5,
max_iter=200,
shuffle=True,
random_state=None,
tol=0.0001,
verbose=False,
warm_start=False,
momentum=0.9,
nesterovs_momentum=True,
early_stopping=False,
validation_fraction=0.1,
beta_1=0.9,
beta_2=0.999,
epsilon=1e-08)
print (npX)
model.fit(npX,npY)
#reg = GradientBoosting(regression = True,treeDepth=2,trees=self.trees,sampling_rate=0.7,loss=self.loss)
#reg.setTargets(["value"])
#reg.learn(facts,examples,bk)
self.model = model
self.AVI()
def __init__(self, rows, columns):
# Get arguments
self.rows = rows
self.columns = columns
# Set initial scores of player 1, 2 = 0
self.score1 = 0
self.score2 = 0
# Set current player to 1
self.curr_player = 1
# Numpy array holding the information about the valency of the nodes(coins)
self.nodes = np.array([4] * ((self.rows) * (self.columns)))
# Numpy array of each edge. They are indexed from left to right starting from the top
# The ID of a given edge is its index in the array
self.num_edges = self.rows * self.columns + (self.rows + 1) * (
self.columns + 1) - 1
# the array
self.edges = np.array([Edge(-1, -1, -1, -1)] * self.num_edges)
# chains. uses num_edges because the number of edges is the max number of chains
self.chains = np.array([Chain(-1)] * self.num_edges)
num_col = self.columns + self.columns + 1 #the number of columns of edges
num_edge_rows = self.rows + self.rows + 1 #the number of rows of edges
cur_edge = 0
ix = 0 #horizontal row count
iy = 0 #vertical row count
# Initialize the edge array
for i in range(0, num_edge_rows):
#horizontal row
if i % 2 == 1:
for j in range(0, self.columns + 1):
if j == 0:
left_node = -1
else:
left_node = cur_edge - (self.rows + 1) - (
2 * self.rows + 1) * ix + self.rows * ix
if j == columns:
right_node = -1
else:
right_node = cur_edge - (self.rows) - (
2 * self.rows + 1) * ix + self.rows * ix
self.chains[cur_edge] = Chain(cur_edge)
self.edges[cur_edge] = Edge(cur_edge, left_node,
right_node, cur_edge)
cur_edge += 1
ix += 1
#vertical row
else:
for j in range(0, self.columns):
if i == 0:
top_node = -1
else:
top_node = cur_edge - self.rows - (self.rows + 1) * iy
if i == num_edge_rows - 1:
bot_node = -1
else:
bot_node = cur_edge - (self.rows + 1) * iy
self.chains[cur_edge] = Chain(cur_edge)
self.edges[cur_edge] = Edge(cur_edge, top_node, bot_node,
cur_edge)
cur_edge += 1
iy += 1
import os
import sys
sys.path.append("../src")
from Chain import Chain
from Likelihood_Planck import Likelihood_Planck
# Prepare the likelihoods
likelihoods = ["commander", "CAMspec", "lowlike"]
clik_dir = "/home/torradocacho/codes/stable/planck_likelihood_1303"
lik = Likelihood_Planck(base_folder=clik_dir, likelihoods=likelihoods)
# Prepare the spectra
CHAINS = "/data/misc/torradocacho/chains"
base_folder = os.path.join(CHAINS, "historicas/aaot/gaussN/07_final")
chain = Chain(os.path.join(base_folder, "gaussN_var_c"))
# 2 best fits
best_fit_points = chain.best_fit(how_many=2)
class_folder = "/home/torradocacho/cosmo/code/class_v1.7.2_external_Pk"
# Overall best fit
best_fit_point = best_fit_points[1]
override_params = {"command": "python "+
os.path.join(class_folder,
"external_Pk/generate_Pk_from_u_gaussN.py")}
spectrum_bf1 = chain.CMBspectrum_from_point(best_fit_point,
class_folder=class_folder,
override_params=override_params,
verbose=True)
override_params = {"P_k_ini type": "analytic_Pk",
metavar="List of 2 parameters to plot")
parser.add_argument("-o",
"--output",
type=str,
dest="output",
nargs=1,
default=None,
metavar="Optional file in which to store the plot.")
parser.add_argument("folders",
type=str,
nargs="+",
metavar="Folders of the chains to be plotted.")
args = parser.parse_args()
# Loading the chains
chains = [Chain(folder) for folder in args.folders]
# Plotting
try:
kwargs = json.loads(args.kwargs)
except ValueError:
raise ValueError(
"The dictionary after '-k'/'--keywords' could not be parsed!" +
" Check the input.")
fig, axarr = plt.subplots(2, 2)
axes_locations = {
"profile": axarr[0, 1],
"mean": axarr[1, 0],
"marginal": axarr[1, 1]
}
for mode, axes in axes_locations.items():
from flask import Flask
from flask import request
from Chain import Chain
from Block import Block
import json
node = Flask(__name__)
blockchain = Chain()
blockchain.start_chain()
i = 0
transaction_queue = [{
'from': 'matteo',
'to': 'kevin',
'value': '3'
}, {
'from': 'annie',
'to': 'john',
'value': '5'
}]
blocks_queue = []
@node.route('/blocks', methods=['GET']) # mostra blocchi nella blockchain
def blocks():
chain = blockchain.get_blockchain()
json_chain = []
for block in chain:
dict = {
'hash': block.hash,
'id': block.id,
'transaction': block.transactions
import os
import sys
sys.path.append("../src")
from Chain import Chain
from plot_lik import plot_lik_2D
base_folder = "./chains"
chain_name = "planck_WP"
chain = Chain(os.path.join(base_folder, chain_name))
labels = {
"omega_b": r"$\omega_\mathrm{B}$",
"omega_cdm": r"$\omega_\mathrm{C}$",
"H0": r"$H_0$",
"tau_reio": r"$\tau_\mathrm{reio}$",
"A_s": r"$A_s$",
"n_s": r"$n_s$",
}
chain.set_parameter_labels(labels)
chain.plot_correlation(params=labels.keys(), save_file="correlations.png")
def AVI(self):
for i in range(self.number_of_iterations):
j = 0
X,Y,bk = [],[],[]
values = {}
fitted_values = {}
while j < self.batch_size:
if self.simulator == "logistics":
state = Logistics(number = self.state_number,start=True)
if not bk:
bk = Logistics.bk
elif self.simulator == "pong":
state = Pong(number = self.state_number,start=True)
if not bk:
bk = Pong.bk
elif self.simulator == "tetris":
state = Tetris(number = self.state_number,start=True)
if not bk:
bk = Tetris.bk
elif self.simulator == "wumpus":
state = Wumpus(number = self.state_number,start=True)
if not bk:
bk = Wumpus.bk
elif self.simulator == "blocks":
state = Blocks_world(number = self.state_number,start=True)
if not bk:
bk = Blocks_world.bk
elif self.simulator == "blackjack":
state = Game(number = self.state_number,start=True)
if not bk:
bk = Game.bk
elif self.simulator == "50chain":
state = Chain(number = self.state_number,start=True)
if not bk:
bk = Chain.bk
elif self.simulator == "net_admin":
state = Admin(number = self.state_number,start=True)
if not bk:
bk = Admin.bk
with open(self.simulator+"_FVI_out.txt","a") as fp:
fp.write("*"*80+"\nstart state: "+str(state.get_state_facts())+"\n")
time_elapsed = 0
within_time = True
start = clock()
trajectory = [(state.state_number,state.get_state_facts())]
while not state.goal():
fp.write("="*80+"\n")
state_action_pair = state.execute_random_action()
state = state_action_pair[0]
fp.write(str(state.get_state_facts())+"\n")
trajectory.append((state.state_number,state.get_state_facts()))
end = clock()
time_elapsed = abs(end-start)
if self.simulator == "logistics" and time_elapsed > 0.5:
within_time = False
break
elif self.simulator == "pong" and time_elapsed > 1000:
within_time = False
break
elif self.simulator == "tetris" and time_elapsed > 10:
within_time = False
break
elif self.simulator == "wumpus" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "blocks" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "blackjack" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "50chain" and time_elapsed > 1:
within_time = False
break
elif self.simulator == "net_id" and time_elapsed > 1:
within_time = False
if within_time:
if i > 0:
self.compute_value_of_trajectory(values,trajectory,AVI=True)
else:
self.compute_value_of_trajectory(values,trajectory,AVI=False)
self.state_number += 1
for key in values:
state = list(key[1])
value = values[key]
#X.append(state)
fitted_values[key] = self.model.predict(np.array([state]))
#Y.append([value])
'''
for key in values:
facts += list(key[1])
example_predicate = "value(s"+str(key[0])+") "+str(values[key])
examples.append(example_predicate)
'''
j += 1
#fitted_values = self.model.predict(np.array(X))
bellman_error = self.compute_bellman_error(values,fitted_values)
with open(self.simulator+"_BEs.txt","a") as f:
f.write("iteration: "+str(i)+" average bellman error: "+str(bellman_error)+"\n")
for key in values:
X.append(list(key[1]))
Y.append(values[key])
npX = np.array(X)
npY = np.array(Y)
self.model.fit(npX,npY)
print "Result = %d" % input
###############################################################################
if __name__ == "__main__":
stringSource1 = StringSource("2")
stringToInt1 = StringToInt(stringSource1)
stringSource2 = StringSource("3")
stringToInt2 = StringToInt(stringSource2)
multiply = Multiply(
[stringToInt1, stringToInt2, stringToInt2, stringToInt1])
intSink = IntSink([stringSource1, multiply])
Chain.Render(intSink)
#
# Errors Detected:
#
# connect too many input stages
# change type of output
# do not fill output parameter
# incorrect output type
# invalid input stage index
# invalid input stage key (GetInputStageValue)
# set invalid output parameter
#
import os
import sys
sys.path.append("../src")
from Chain import Chain
from plot_lik import plot_lik_2D
base_folder = "./chains"
chain = "planck_WP"
chains = [Chain(os.path.join(base_folder, chain))]
params = ["H0", "omega_b"]
labels = [r"$H_0$", r"$\omega_b$"]
modes = ["marginal", "profile"]
for mode in modes:
plot_lik_2D(mode,
chains,
params=params,
labels=labels,
format="-loglik",
save="./%s_%s_%s.png" % (params[0], params[1], mode))
# self.age = age
# student.name = "Lucy"
# student.sex = '男'
student.age = 90
print(student.age)
print(student2.age)
print(student)
# print(student.name)
# 动态绑定方法到实例
# student.set_age = MethodType(set_age, student)
# student.set_age(20)
# print(student.age)
url1 = Chain().users.test
print(url1)
url = Chain().users('mac').photo('testphoto').repos
print(url)
# 使用type创建class
def fn(self, name='world'):
print('Hello, %s.' % name)
Hello = type('Hello', (object, ), dict(hello=fn))
h = Hello()
h.hello('Mac')