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Output cosmetics

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This commit is contained in:
Artur Meski
2016-03-04 20:52:02 +01:00
parent 45b6db12c4
commit dc482781e2
2 changed files with 24 additions and 41 deletions
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24
rctsys.py
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@@ -114,13 +114,13 @@ class ContextAutomaton(object):
str_transition = str(transition[0]) + " --( " str_transition = str(transition[0]) + " --( "
str_transition += self.context2str(transition[1]) str_transition += self.context2str(transition[1])
str_transition += " )--> " + str(transition[2]) str_transition += " )--> " + str(transition[2])
print("\t- " + str_transition) print(" - " + str_transition)
def show_states(self): def show_states(self):
init_state_name = self.get_init_state_name() init_state_name = self.get_init_state_name()
print("[*] Context automaton states:") print("[*] Context automaton states:")
for state in self._states: for state in self._states:
print("\t- " + state, end="") print(" - " + state, end="")
if state == init_state_name: if state == init_state_name:
print(" [init]") print(" [init]")
else: else:
@@ -309,10 +309,14 @@ class ReactionSystem(object):
def show_reactions(self, soft=False): def show_reactions(self, soft=False):
print("[*] Reactions:") print("[*] Reactions:")
if soft and len(self.reactions) > 50: if soft and len(self.reactions) > 50:
print("\t -> there are more than 50 reactions (" + str(len(self.reactions)) + ")") print(" -> there are more than 50 reactions (" + str(len(self.reactions)) + ")")
else: else:
print(" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants"," inhibitors"," products"))
for reaction in self.reactions: for reaction in self.reactions:
print("\t - ( R={" + self.state_to_str(reaction[0]) + "}, \tI={" + self.state_to_str(reaction[1]) + "}, \tP={" + self.state_to_str(reaction[2]) + "} )") # print("\t( R={" + self.state_to_str(reaction[0]) + "}, I={" + self.state_to_str(reaction[1]) + "}, P={" + self.state_to_str(reaction[2]) + "} )")
print(" "*2 + "- {0: ^35}{1: ^25}{2: ^15}".format("{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }"))
def show_background_set(self): def show_background_set(self):
print("[*] Background set: {" + self.entities_names_set_to_str(self.background_set) + "}") print("[*] Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
@@ -321,7 +325,7 @@ class ReactionSystem(object):
if len(self.init_contexts) > 0: if len(self.init_contexts) > 0:
print("[*] Initial context sets:") print("[*] Initial context sets:")
for ctx in self.init_contexts: for ctx in self.init_contexts:
print("\t - {" + self.entities_ids_set_to_str(ctx) + "}") print(" - {" + self.entities_ids_set_to_str(ctx) + "}")
def show_context_entities(self): def show_context_entities(self):
if len(self.context_entities) > 0: if len(self.context_entities) > 0:
@@ -523,7 +527,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def state_to_str(self, state): def state_to_str(self, state):
s = "" s = ""
for ent,level in state: for ent,level in state:
s += str((self.get_entity_name(ent),level)) + ", " s += self.get_entity_name(ent) + "=" + str(level) + ", "
s = s[:-2] s = s[:-2]
return s return s
@@ -535,20 +539,20 @@ class ReactionSystemWithConcentrations(ReactionSystem):
for param_ent,reactions in self.meta_reactions.items(): for param_ent,reactions in self.meta_reactions.items():
for r_type,command,reactants,inhibitors in reactions: for r_type,command,reactants,inhibitors in reactions:
if r_type == "inc" or r_type == "dec": if r_type == "inc" or r_type == "dec":
print("\t - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + \ print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + \
" ) Command=( " + self.get_entity_name(command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, \tI={" + self.state_to_str(inhibitors) + "} )") " ) Command=( " + self.get_entity_name(command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
else: else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type)) raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show_max_concentrations(self): def show_max_concentrations(self):
print("[*] Maximal allowed concentration levels (for optimized translation to RS):") print("[*] Maximal allowed concentration levels (for optimized translation to RS):")
for e,max_conc in self.max_conc_per_ent.items(): for e,max_conc in self.max_conc_per_ent.items():
print("\t - {0:>20} = {1:<6}".format(self.get_entity_name(e),max_conc)) print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e),max_conc))
def show_permanent_entities(self): def show_permanent_entities(self):
print("[*] Permanent entities:") print("[*] Permanent entities:")
for e,inhibitors in self.permanent_entities.items(): for e,inhibitors in self.permanent_entities.items():
print("\t - {0:>20}: {1:<6}".format(self.get_entity_name(e),"I={" + self.state_to_str(inhibitors) + "}")) print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ","I={" + self.state_to_str(inhibitors) + "}"))
def show(self, soft=False): def show(self, soft=False):
self.show_background_set() self.show_background_set()

41
smtcheckerrsc.py
View File

@@ -7,6 +7,7 @@ from time import time
from sys import stdout from sys import stdout
from itertools import chain from itertools import chain
import resource import resource
from colour import *
# def simplify(x): # def simplify(x):
# return x # return x
@@ -138,29 +139,6 @@ class SmtCheckerRSC(object):
enc_inhibitors = simplify(And(enc_inhibitors, enc_inhibitors = simplify(And(enc_inhibitors,
And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration))) And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
# if r_type == "inc":
# # depending on if the value of the command entity is greater in the context or in the current RS state
# # we choose to increment by the greater value from v or v_ctx (this is because we take the max value).
# enc_products = Or(
# And(self.v_ctx[level][command_entity] >= self.v[level][command_entity],
# self.v[level+1][prod_entity] == If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity])+self.v_ctx[level][command_entity]),
# And(self.v[level][command_entity] > self.v_ctx[level][command_entity],
# self.v[level+1][prod_entity] == If(self.v[level][prod_entity]>self.v_ctx[level][command_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity])+self.v[level][command_entity]))
#
# elif r_type == "dec":
# # same happens here, but we decrement with the maximum value encoded at v or v_ctx.
# enc_products = Or(
# And(self.v_ctx[level][command_entity] >= self.v[level][command_entity],
# self.v[level+1][prod_entity] == If(self.v[level][prod_entity]>self.v_ctx[level][command_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity])-self.v_ctx[level][command_entity]),
# And(self.v[level][command_entity] > self.v_ctx[level][command_entity],
# self.v[level+1][prod_entity] == If(self.v[level][prod_entity]>self.v_ctx[level][command_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity])-self.v[level][command_entity]))
#
# if r_type == "inc":
# enc_products = self.v[level+1][prod_entity] == self.v[level][prod_entity]+1
#
# elif r_type == "dec":
# enc_products = self.v[level+1][prod_entity] == self.v[level][prod_entity]-1
if r_type == "inc": if r_type == "inc":
enc_products = simplify(self.v[level+1][prod_entity] == \ enc_products = simplify(self.v[level+1][prod_entity] == \
If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) + \ If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) + \
@@ -321,7 +299,7 @@ class SmtCheckerRSC(object):
for level in range(max_level+1): for level in range(max_level+1):
print("\n{:-^70}".format("[ level=" + repr(level) + " ]")) print("\n{: >70}".format("[ level=" + repr(level) + " ]"))
print(" State: {", end=""), print(" State: {", end=""),
for var_id in range(len(self.v[level])): for var_id in range(len(self.v[level])):
@@ -365,24 +343,25 @@ class SmtCheckerRSC(object):
stdout.flush() stdout.flush()
# reachability test: # reachability test:
print("[i] Adding the reachability test...") print("[" + colour_str(C_BOLD, "i") + "] Adding the reachability test...")
self.solver.push() self.solver.push()
self.solver.add(self.enc_state_with_blocking(current_level,state)) self.solver.add(self.enc_state_with_blocking(current_level,state))
result = self.solver.check() result = self.solver.check()
if result == sat: if result == sat:
print("\n[+] SAT at level=" + str(current_level)) print("[" + colour_str(C_BOLD, "+") + "] " + colour_str(C_GREEN, "SAT at level=" + str(current_level)))
if print_witness: if print_witness:
print("\n{:=^70}".format("[ WITNESS ]"))
self.decode_witness(current_level) self.decode_witness(current_level)
break break
else: else:
self.solver.pop() self.solver.pop()
print("[i] Unrolling the transition relation") print("[" + colour_str(C_BOLD, "i") + "] Unrolling the transition relation")
self.solver.add(self.enc_transition_relation(current_level)) self.solver.add(self.enc_transition_relation(current_level))
print("\n{:-^70}".format("[ level=" + str(current_level) + " done ]")) print("{:->70}".format("[ level=" + str(current_level) + " done ]"))
current_level += 1 current_level += 1
if current_level > max_level: if current_level > max_level:
@@ -394,10 +373,10 @@ class SmtCheckerRSC(object):
stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime stop = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.verification_time = stop-start self.verification_time = stop-start
print() print()
print("\n[i] {:_>60}".format(" Time: " + repr(self.verification_time) + " s")) print("\n[i] {: >60}".format(" Time: " + repr(self.verification_time) + " s"))
if print_mem: if print_mem:
print("[i] {:_>60}".format(" Memory: " + repr(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)) + " MB")) print("[i] {: >60}".format(" Memory: " + repr(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)) + " MB"))
def get_verification_time(self): def get_verification_time(self):
return self.verification_time return self.verification_time
@@ -431,7 +410,7 @@ class SmtCheckerRSC(object):
result = self.solver.check() result = self.solver.check()
if result == sat: if result == sat:
print("\n[+] SAT at level=" + str(current_level)) print("\n[+] " + colour_str(C_RED, "SAT at level=" + str(current_level)))
if print_witness: if print_witness:
self.decode_witness(current_level) self.decode_witness(current_level)
break break