def render(self, field, key, value, REQUEST, render_prefix=None):
"""
This is where most things happens
"""
main_content = ""
here = REQUEST['here']
selection_name = field.get_value('selection_name')
default_params = field.get_value('default_params')
chart_title = field.get_value('chart_title')
data_method = field.get_value('data_method')
chart_style = field.get_value('chart_style')
x_title = field.get_value('x_title')
y_title = field.get_value('y_title')
bg_transparent = field.get_value('bg_transparent')
selection = here.portal_selections.getSelectionFor(selection_name, REQUEST=REQUEST)
LOG('ZGDChart.render',0,'selection: %s, selection_name: %s' % (str(selection),
str(selection_name)))
# This is the default data, this is just in the case there is not method given
data = {'chart_data':[]}
# Retrieve the data with the data_method
if hasattr(here,data_method):
LOG('ZGDChart.render',0,'found method')
data_method = getattr(here,data_method)
data['chart_data'] = data_method()
data['chart_parameter'] = {'zgdchart_runtime_title':chart_title,
'zgdchart_runtime_xtitle':x_title,
'zgdchart_runtime_ytitle':y_title,
'zgdchart_runtime_type':'Line_3D',
'zgdchart_runtime_bg_transparent':bg_transparent}
# Creation selection if needed
if selection is None:
selection = Selection(selection_name, params=data)
else:
LOG('ZGDChart.render',0,'selection is not None')
kw = {'params':data}
selection.edit(**kw)
here.portal_selections.setSelectionFor(selection_name, selection, REQUEST=REQUEST)
if len(data['chart_data']) > 0:
main_content = """\
<div class="ChartContent">
<table border="0" cellpadding="0" cellspacing="0"">
<tr>
<td valign="middle" align="center" nowrap>
<img src="%s" title="Chart" border="0" alt="img"/">
</td>
</tr>
</table>
</div>""" % str(chart_style + '?selection_name=' + selection_name)
return main_content
def main():
args = argsParser()
args.parse('args.xml')
if args.fitnessFunction == "euclidean" : fitOp = EuclideanDistFit(args.input1, args.input2)
elif args.fitnessFunction == "manhattan" : fitOp = ManhattanDistFit(args.input1, args.input2)
elif args.fitnessFunction == "minkowski" : fitOp = MinkowskiDistFit(args.input1, args.input2, args.p)
elif args.fitnessFunction == "linear" : fitOp = LinearInterpolation(args.input1, args.input2, args.euclF, args.manhF)
else : raise "Something went wrong while assigning the fitness function"
#
if args.selection == "tournament" : selOp = Selection.tournament
elif args.selection == "elimination": selOp = Selection.elimination
else : raise "Something went wrong while assigning the selection operator"
if args.elitism == 0: Selection.setElitism(0)
elif args.elitism == 1: Selection.setElitism(1)
else : raise "Something went wrong while assigning elitism"
crossOp = Crossover.crossover
mutationOp = Mutation.mutation
if args.batch == 1:
p = Population(args.populationSize, fitOp, selOp, crossOp, mutationOp)
p.evaluateAll()
run (p, args)
writeOut(args.outputFile, p)
else:
for i in range(0, args.batch):
print "\nBatch: %d/%d" %(i+1, args.batch)
p = Population(args.populationSize, fitOp, selOp, crossOp, mutationOp)
p.evaluateAll()
run (p, args)
writeOutBatch(i+1, p)
def __sort(algs, data):
if 'insertion' == algs:
Insertion.sort(data)
if 'insertion_advance' == algs:
Insertion.sort_advance(data)
if 'selection' == algs:
Selection.sort(data)
if 'shell' == algs:
Shell.sort(data)
if 'merge' == algs:
Merge.sort(data)
def solve(self):
'''
evolution process of differential evolution algorithm
'''
self.t = 0
self.initialize()
for i in range(0, self.sizepop):
self.evaluate(self.population[i])
self.fitness[i] = self.population[i].fitness
best = np.max(self.fitness)
bestIndex = np.argmax(self.fitness)
self.best = copy.deepcopy(self.population[bestIndex])
self.avefitness = np.mean(self.fitness)
self.trace[self.t, 0] = (1 - self.best.fitness) / self.best.fitness
self.trace[self.t, 1] = (1 - self.avefitness) / self.avefitness
print("当前代数 %d: 最优个体适应度值: %f; 当代平均适应度值 %f; " %
(self.t, self.trace[self.t, 0], self.trace[self.t, 1]))
# print("最有个体:")
# print(self.best.chrom)
while (self.t < self.MAXGEN - 1):
self.t += 1
for i in range(0, self.sizepop):
# 遗传操作
mutation = Mutation(self.vardim, self.bound, self.sizepop,
self.population, self.params)
vi = mutation.Random_3_different_current_mutation(i)
crossover = Crossover(self.vardim, self.population,
self.params)
ui = crossover.Standard_Crossover(i, vi)
selection = Selection(self.population)
xi_next = selection.selectionOperation(i, ui)
self.population[i] = xi_next
for i in range(0, self.sizepop):
self.evaluate(self.population[i])
self.fitness[i] = self.population[i].fitness
best = np.max(self.fitness)
bestIndex = np.argmax(self.fitness)
if best > self.best.fitness:
self.best = copy.deepcopy(self.population[bestIndex])
self.avefitness = np.mean(self.fitness)
self.trace[self.t, 0] = (1 - self.best.fitness) / self.best.fitness
self.trace[self.t, 1] = (1 - self.avefitness) / self.avefitness
print("当前代数 %d: 最优个体适应度值: %f; 当代平均适应度值 %f; " %
(self.t, self.trace[self.t, 0], self.trace[self.t, 1]))
# print("最优个体:")
# print(self.best.chrom)
print("Optimal function value is: %f; " % self.trace[self.t, 0])
print("Optimal solution is:")
print(self.best.chrom)
self.printResult()
def download(self, selection_name=None, data_method=None, REQUEST=None, **kw):
"""
This is where we actually render the chart. The main interest
of doing like this is to accelerate initial rendering
TODO:
- add minimal security here
- implement all pychart options (PNG, PS, SVG, etc.)
- implement all standard parameters
"""
# Get the applicable selection
selection = self.portal_selections.getSelectionFor(selection_name, REQUEST=REQUEST)
# If selection is None, create a new one
if selection is None:
selection = Selection(selection_name)
# Get the data method if defined
if data_method is not None:
here = REQUEST.get('here', self)
data_method = getattr(here, data_method, None)
# This is the default data, this is just in the case there is not method given
if data_method is None:
data = selection()
else:
data = selection(data_method=data_method)
# Now call the script - XXX implement bindings properly here
output = self._exec(here=self, pychart=pychart, data=data)
# And return result
return output
def __init__(self,
generator,
fitness,
mutation,
sizeOfPopulation,
genPopulation,
selection=None,
crossover=None,
numberChromosome=None,
epoche=100,
error=0.001,
stopFunctionChange=False,
data=None,
**kwargs):
self.generator = generator
self.fitness = fitness
if selection is None:
selection = Selection('empty')
self.selection = selection
if crossover is None:
crossover = Crossover('empty')
self.crossover = crossover
self.mutation = mutation
self.sizeOfPopulation = sizeOfPopulation
self.stopFunctionChange = stopFunctionChange
self.populationGen = genPopulation
self.numberChromosome = numberChromosome
self.epoche = epoche
self.error = error
self.data = data
self.otherArgs = kwargs
def _loop(self):
done = False
clock = pg.time.Clock()
while not done:
clock.tick(FPS)
self._drawMe()
pg.display.flip()
for event in pg.event.get():
if event.type == pg.VIDEORESIZE:
self._resize(event.w, event.h)
if event.type == pg.QUIT:
done = True
break
if event.type == pg.KEYDOWN:
if event.key == pg.K_s:
self._solve()
if event.key == pg.K_z:
self._wipe()
if event.key == pg.K_r:
self._reset()
if event.key == pg.K_a:
done = True
break
if event.type == pg.MOUSEBUTTONDOWN:
self._mouseClicHandeler()
from Selection import Selection
pg.quit()
Selection()
def __init__(self, name, deck_name, game_config):
self.deck = Deck(deck_name)
self.home_pile = HomePile(game_config.home_pile_size)
self.cell_cards = CellCards(self.home_pile)
self.stock_pile = StockPile()
self.right_hand = RightHand()
self.discard_pile = DiscardPile()
self.home_pile.take_from(self.deck)
self.cell_cards.take_from(self.deck)
self.stock_pile.take_from(self.deck)
self.set_locations()
# Move cards to their proper locations
self.home_pile.calibrate()
self.cell_cards.calibrate()
self.stock_pile.calibrate()
# Start out with cell cards face down
for cell in self.cell_cards.each_cell():
cell.face_down()
#
self.selection = Selection()
self.drawables = [self.home_pile,
self.cell_cards,
self.stock_pile,
self.discard_pile,
self.right_hand,
self.selection]
self.clickables = [self.home_pile,
self.cell_cards,
self.discard_pile]
self.updateables = []
self.xxxcount = 0
self.score = 0
self.cards_in_transit = []
self.name = name
louie.connect(self.card_grabbed, Card.grabbed)
louie.connect(self.card_thrown, Card.thrown)
louie.connect(self.home_emptied, HomePile.emptied)
def __init__(self, parent, mainmesh=True, hfs=[]):
self.mainmesh = mainmesh
self.parent = parent
self.fab_directions = [0, 1] #Initiate list of fabircation directions
for i in range(1, self.parent.noc - 1):
self.fab_directions.insert(1, 1)
if len(hfs) == 0:
self.height_fields = get_random_height_fields(
self.parent.dim,
self.parent.noc) #Initiate a random joint geometry
else:
self.height_fields = hfs
if self.mainmesh: self.select = Selection(self)
self.voxel_matrix_from_height_fields(first=True)
def createDummyTask(conn):
ts = time.time()
isodate = datetime.datetime.fromtimestamp(ts, None)
accCol = conn["user"]["account"]
acc = accCol.find_one({})
accid = str(acc["_id"])
coll = conn["experiment"]["task"]
sell = list()
selid = str(Selection.createDummySelection(conn))
sell.append(selid)
post = { \
"name": "Dummy task", \
"status": "Active", \
"start": isodate, \
"end": isodate, \
"account_id": accid, \
"parameters": "a2+b2=c2", \
"selection_ids": sell, \
"result_file": "None" \
}
coll.insert(post)
coll.ensure_index("name", unique=True)
coll.ensure_index("account_id")
from Selection import Selection
if __name__ == '__main__':
Selection()
def __init__(self, x, y):
super().__init__(x, y)
self.image = Sprites.CURSOR
self.collides = False
self.selection_1 = Selection(0, 0)
self.selection_2 = Selection(0, 0)
from Mutation import Mutation
import utils
aptamerType = str(sys.argv[1])
aptamerNum = int(sys.argv[2])
seqLength = int(sys.argv[3])
selectionThreshold = long(sys.argv[4])
roundNum = int(sys.argv[5])
pcrCycleNum = int(sys.argv[6])
pcrYield = float(sys.argv[7])
pcrErrorRate = float(sys.argv[8])
outputFileNames = str(sys.argv[9])
# Instantiating classes
Apt = Aptamers()
S = Selection()
Amplify = Amplification()
Mut = Mutation()
# SELEX simulation based on random aptamer assignment, hamming-based definite selection, and
# non-ideal stochastic amplfication with no bias.
for r in range(roundNum):
if(r==0):
if(aptamerType == 'DNA'):
alphabetSet = 'ACGT'
aptamerSeqs, initialSeqNum = Apt.optimumAptamerGenerator(aptamerNum, alphabetSet, seqLength)
elif(aptamerType == 'RNA'):
alphabetSet = 'ACGU'
aptamerSeqs, initialSeqNum = Apt.optimumAptamerGenerator(aptamerNum, alphabetSet, seqLength)
else:
print("Error: Simulation of %.s aptamers not supported" %aptamerType)
def __init__(self, **kwargs):
for key, value in kwargs.items():
if key == 'genetarion':
self.generation_size = value
elif key == 'population':
self.population_size = value
elif key == 'limit_population':
self.limit_population = value
elif key == 'crossover_rate':
self.crossover_rate = value
elif key == 'mutation_rate':
self.mutation_rate = value
elif key == 'map_points':
self.map_points = value
elif key == 'max_coust':
self.max_coust = value
elif key == 'coust_rate':
self.coust_rate = value
elif key == 'prizes_rate':
self.prizes_rate = value
elif key == 'start_point':
self.start_point = value
elif key == 'end_point':
self.end_point = value
elif key == 'prizes':
prizes = np.loadtxt(value)
self.prizes = prizes[:, 1]
elif key == 'initial_cromossome':
self.initial_cromossome = value
self.best_route = value
self.receive_route = True
# as variáveis
# self.generation_size = genetarion
# self.population_size = population
# self.limit_population = limit_population
# self.crossover_rate = crossover_rate
# self.mutation_rate = mutation_rate
# self.map_points = map_points
# self.max_coust = max_coust
# self.start_point = np.array([start_point])
# self.end_point = np.array([end_point])
# self.prizes = np.loadtxt(prizes)
self.mapa = np.loadtxt(self.map_points)
self.distance_matrix_calculate()
if 'initial_cromossome' not in locals():
self.initial_cromossome = np.arange(self.mapa.shape[0])
self.receive_route = False
if self.start_point != self.end_point:
self.initial_cromossome = np.delete(
self.initial_cromossome, [self.start_point, self.end_point])
else:
self.initial_cromossome = np.delete(self.initial_cromossome,
[self.start_point])
self.mutation_object = Mutation(self.max_coust, self.prizes)
self.mutation = self.mutation_object.scramble
self.crossover_class = Crossover()
self.crossover = self.crossover_class.PMX
self.Population = Population(self.start_point, self.end_point,
self.med_custo, self.max_coust)
self.Selection_object = Selection()
self.selection = self.Selection_object.tournament
def __init__( self, board, primaryObjectFamilies, secondaryObjectFamilies, primarySurfaceFamilies, secondarySurfaceFamilies ):
gtk.HBox.__init__( self, False, 0 )
self.board = board
self.board.registerView( self )
self.selection = Selection( self )
self.mouseManager = MouseManager.MouseManager( self )
for family in primaryObjectFamilies:
self.selection.addObjects( family )
for family in primarySurfaceFamilies:
self.selection.addSurfaces( family )
self.__scale = MapView.__pixelPerUnit * 4
self.__translateX = 0
self.__translateY = 0
self.__sisterViews = list()
self.drawingArea = gtk.DrawingArea()
self.drawingArea.connect( "expose-event", self.__onExposeEvent )
self.drawingArea.set_events(
gtk.gdk.EXPOSURE_MASK |
gtk.gdk.LEAVE_NOTIFY_MASK |
gtk.gdk.BUTTON_PRESS_MASK |
gtk.gdk.BUTTON_RELEASE_MASK |
gtk.gdk.POINTER_MOTION_MASK |
gtk.gdk.POINTER_MOTION_HINT_MASK
)
self.drawingArea.show()
toolBar = gtk.Toolbar()
toolBar.set_orientation( gtk.ORIENTATION_VERTICAL )
self.__objectFamilies = primaryObjectFamilies + secondaryObjectFamilies
self.__surfaces = list()
for family in secondarySurfaceFamilies + primarySurfaceFamilies:
for surface in GameItemTypes.surfaces[ family ]:
self.__surfaces.append( surface )
toolBar.append_item( _( "Select/Move" ), "", "", None, lambda widget: self.resetMouseManager() )
for family in primarySurfaceFamilies:
for surface in GameItemTypes.surfaces[ family ]:
if GameItemTypes.attributes[ surface ][ "BuiltByLengths" ]:
menu = gtk.Menu()
item = gtk.MenuItem( _( "Length" ) )
menu.append( item )
item.connect( "activate", lambda widget, surfaceType: self.mouseManager.setState( MouseManager.StartInsertSurface, surfaceType, MouseManager.SurfaceLength() ), surface )
item.show()
item = gtk.MenuItem( _( "Rectangle" ) )
menu.append( item )
item.connect( "activate", lambda widget, surfaceType: self.mouseManager.setState( MouseManager.StartInsertSurface, surfaceType, MouseManager.SurfaceRectangle() ), surface )
item.show()
toolBar.append_item( _( surface ), "", "", None, lambda widget, menu: menu.popup( None, None, None, 3, 0 ), menu )
else:
toolBar.append_item( _( surface ), "", "", None, lambda widget, surfaceType: self.mouseManager.setState( MouseManager.StartInsertSurface, surfaceType, MouseManager.SurfaceRectangle() ), surface )
for family in primaryObjectFamilies:
for category, subCategories in GameItemTypes.objects[ family ].iteritems():
menu = gtk.Menu()
for subCategory, buildingTypes in subCategories.iteritems():
for buildingType in buildingTypes:
item = gtk.MenuItem( _( buildingType ) )
menu.append( item )
item.connect( "activate", lambda widget, buildingType: self.mouseManager.setState( MouseManager.InsertingObject, buildingType ), buildingType )
if not self.board.isAvailable( buildingType ):
item.set_sensitive( False )
item.show()
toolBar.append_item( _( category ), "", "", None, lambda widget, menu: menu.popup( None, None, None, 3, 0 ), menu )
toolBar.show()
self.pack_end( toolBar, False, False, 2 )
self.pack_start( self.drawingArea, True, True, 2 )
def __init__(self,
map_points,
iterations,
size_population,
beta,
alfa,
cost_rate,
prizes_rate,
prizes,
max_cost,
start_point,
end_point,
depositos=[]):
self.map_points = np.loadtxt(map_points)
self.iterations = iterations
self.size_population = size_population
self.beta = beta
self.alfa = alfa
self.cost_rate = np.array(cost_rate)
self.prizes_rate = prizes_rate
self.prizes = np.loadtxt(prizes)[:, 1]
self.max_cost = np.array(max_cost)
self.start_point = start_point
self.end_point = end_point
self.depositos = depositos
self.particles = []
self.number_agents = len(max_cost)
self.distance = calculate_distances(self.map_points)
self.functionObject = FunctionObjective(self.map_points, self.prizes)
self.FO = self.functionObject.FO
self.mensureCost = self.functionObject.med_custo
self.methodInsertRemoveChromosome = self.functionObject.coust_insert
self.allElementsMap = np.arange(self.map_points.shape[0])
self.allElementsMap = self.allElementsMap[self.number_agents:]
# removendo depositos
deposits = [x for x in self.start_point]
deposits += [x for x in self.end_point if x not in deposits]
deposits = np.unique(np.array(deposits))
self.initialChromossome = np.arange(self.map_points.shape[0])
self.initialChromossome = np.delete(self.initialChromossome,
self.depositos)
self.allElementsMap = np.copy(self.initialChromossome)
self.mutationObject = Mutation(self.mensureCost, self.max_cost,
self.prizes)
self.mutation = self.mutationObject.scramble
self.crossoverObject = Crossover()
self.crossover = self.crossoverObject.cross_TOPMD
self.PopulationObject = Population(self.start_point, self.end_point,
self.mensureCost, self.max_cost,
self.distance)
self.SelectionObject = Selection()
self.selection = self.SelectionObject.tournament
solutions = self.PopulationObject.initializeTopMdGreed2(
self.initialChromossome, self.size_population, self.number_agents,
1)
for s in solutions:
particle = Particle(route=s,
mensure_function=self.mensureCost,
fitness_function=self.FO)
self.particles.append(particle)
class Player:
""" A player in the game. """
finished = louie.Signal()
def __init__(self, name, deck_name, game_config):
self.deck = Deck(deck_name)
self.home_pile = HomePile(game_config.home_pile_size)
self.cell_cards = CellCards(self.home_pile)
self.stock_pile = StockPile()
self.right_hand = RightHand()
self.discard_pile = DiscardPile()
self.home_pile.take_from(self.deck)
self.cell_cards.take_from(self.deck)
self.stock_pile.take_from(self.deck)
self.set_locations()
# Move cards to their proper locations
self.home_pile.calibrate()
self.cell_cards.calibrate()
self.stock_pile.calibrate()
# Start out with cell cards face down
for cell in self.cell_cards.each_cell():
cell.face_down()
#
self.selection = Selection()
self.drawables = [self.home_pile,
self.cell_cards,
self.stock_pile,
self.discard_pile,
self.right_hand,
self.selection]
self.clickables = [self.home_pile,
self.cell_cards,
self.discard_pile]
self.updateables = []
self.xxxcount = 0
self.score = 0
self.cards_in_transit = []
self.name = name
louie.connect(self.card_grabbed, Card.grabbed)
louie.connect(self.card_thrown, Card.thrown)
louie.connect(self.home_emptied, HomePile.emptied)
def draw(self, surface):
for drawable in self.drawables:
drawable.draw(surface)
for card in self.cards_in_transit:
card.draw(surface)
def set_locations(self):
""" Position cards """
some_card = self.home_pile.top_card()
card_width, card_height = some_card.rect.width, some_card.rect.height
left_margin, top_margin = 15, 450
hand_top_margin = top_margin + card_height + 10
x, y = left_margin, top_margin
# Top row
self.home_pile.move_to(x, y)
x += card_width * 1.7
distance_between = card_width * 1.3
self.cell_cards.move_to(x, y, distance_between)
x = left_margin + card_width * 0.2
y = hand_top_margin
# Bottom row
self.stock_pile.move_to(x, y)
x += card_width * 1.5
self.discard_pile.move_to(x, y)
x += card_width * 1.5
self.right_hand.move_to(x, y, 40)
def update(self):
for updateable in self.updateables:
updateable.update()
for card in self.cards_in_transit:
card.update()
def handle(self, event):
""" Handle events that the player knows about. """
if event.type == pygame.MOUSEBUTTONDOWN:
if event.button == 1:
self.handle_left_mouse_down(event)
elif event.button == 3:
self.handle_right_mouse_down(event)
elif event.type == pygame.KEYDOWN:
if event.key == pygame.K_SPACE:
self.handle_space_bar()
def handle_left_mouse_down(self, event):
""" Handle a left click. """
x, y = event.pos[0], event.pos[1]
for clickable in self.clickables:
card = clickable.get_card(x, y)
if card is not None:
if not self.selection.empty() and \
self.selection.card == card:
# Clear the selection if the card is already selected
self.selection.clear()
else:
# Otherwise select the card
self.selection.set(card, clickable)
return
# Stock pile clicks
if self.stock_pile.contains(x, y):
self.deal_card()
def handle_right_mouse_down(self, event):
""" Handle a right click. """
self.deal_card()
def handle_space_bar(self):
""" Handle a space bar keypress. """
self.deal_card()
def deal_card(self):
""" Shuffle from stock_pile to discard_pile
Place in hand if count < 3,
otherwise place in discard pile, count = 0 """
if self.xxxcount != 0 and self.stock_pile.cards.empty():
self.xxxcount = 3
self.xxxcount += 1
if self.xxxcount == 4:
self.discard_pile.take_from(self.right_hand)
self.discard_pile.calibrate()
self.xxxcount = 0
if self.has_selection() and \
self.selection.home == self.discard_pile:
# Clear the selection if it's the discard pile
self.clear_selection()
else:
if self.stock_pile.cards.empty():
self.stock_pile.take_from(self.discard_pile.cards)
self.stock_pile.calibrate()
self.right_hand.take_from(self.stock_pile.cards)
self.right_hand.calibrate()
def home_emptied(self):
louie.send(Player.finished)
def inc_score(self):
self.score += 1
def get_score(self):
""" Returns the total score """
return self.num_good_cards() - self.num_bad_cards() * 2
def num_good_cards(self):
""" Returns the number of cards put out """
return self.score
def num_bad_cards(self):
""" Returns the number of cards still in the home pile """
return self.home_pile.cards.num_cards()
def card_thrown(self, card):
self.cards_in_transit.append(card)
def card_grabbed(self, card):
self.cards_in_transit.remove(card)
def get_selection(self):
""" Returns the current selection. """
return self.selection
def has_selection(self):
""" Returns true if there is a card selected. """
return not self.selection.empty()
def clear_selection(self):
self.selection.clear()
def get_name(self):
return self.name
def flip_cell(self, cell_index):
self.cell_cards.get_cell(cell_index).flip()
def time(alg, a):
timer = Stopwatch()
if alg == "Insertion": Insertion.sort(a)
if alg == "Selection": Selection.sort(a)
if alg == "Shell": Shell.sort(a)
return timer.elapsedTime()
roundNum = settings.getint('general', 'number_of_rounds')
outputFileNames = settings.get('general', 'experiment_name')
samplingSize = settings.getint('general', 'sampling_size')
post_process = settings.get('general', 'post_process')
selectionThreshold = settings.getint('selectionparams', 'scale')
distanceMeasure = settings.get('selectionparams', 'distance')
stringency = settings.getint('selectionparams', 'stringency')
pcrCycleNum = settings.getint('amplificationparams', 'number_of_pcr')
pcrYield = settings.getfloat('amplificationparams', 'pcr_efficiency')
pcrerrorRate = settings.getfloat('amplificationparams', 'pcr_error_rate')
# Instantiating the appropriate classes
Apt = Aptamers()
S = Selection()
Amplify = Amplification()
Mut = Mutation()
if (distanceMeasure == "hamming"):
# SELEX simulation based on random aptamer assignment, hamming-based stochastic selection, and
# non-ideal stochastic amplfication with pyrimidine-based bias.
for r in range(roundNum):
if (r == 0):
if (aptamerType == 'DNA'):
alphabetSet = 'ACGT'
aptamerSeqs, initialSeqNum = Apt.optimumAptamerGenerator(
aptamerNum, alphabetSet, seqLength)
elif (aptamerType == 'RNA'):
alphabetSet = 'ACGU'
aptamerSeqs, initialSeqNum = Apt.optimumAptamerGenerator(
def __init__(self, **kwargs):
for key, value in kwargs.items():
if key == 'genetarion':
self.generation_size = value
elif key == 'population':
self.population_size = value
elif key == 'limit_population':
self.limit_population = value
elif key == 'crossover_rate':
self.crossover_rate = value
elif key == 'mutation_rate':
self.mutation_rate = value
elif key == 'map_points':
self.map_points = value
elif key == 'max_coust':
self.max_coust = np.array(value)
elif key == 'coust_rate':
self.coust_rate = value
elif key == 'prizes_rate':
self.prizes_rate = value
elif key == 'start_point':
self.start_point = value
elif key == 'end_point':
self.end_point = value
elif key == 'prizes':
prizes = np.loadtxt(value)
self.prizes = prizes[:, 1]
elif key == 'initial_cromossome':
self.initial_cromossome = value
self.best_route = value
self.receive_route = True
elif key == 'number_agents':
self.number_agents = value
self.mapa = np.loadtxt(self.map_points)
self.distance_matrix_calculate()
self.FunctionObject = FunctionObjective(self.mapa, self.prizes)
self.function_objective = self.FunctionObject.FO
self.med_custo = self.FunctionObject.med_custo
self.function_insert_remove = self.FunctionObject.coust_insert
# todos os pontos de um mapa
self.all_elements = np.arange(self.mapa.shape[0])
if 'initial_cromossome' not in locals():
self.initial_cromossome = np.arange(self.mapa.shape[0])
self.receive_route = False
if self.start_point != self.end_point:
self.initial_cromossome = np.delete(
self.initial_cromossome, [self.start_point, self.end_point])
else:
self.initial_cromossome = np.delete(self.initial_cromossome,
[self.start_point])
self.mutation_object = Mutation(self.med_custo, self.max_coust,
self.prizes)
self.mutation = self.mutation_object.scramble
self.crossover_class = Crossover()
self.crossover = self.crossover_class.cross_TOP
self.Population = Population(self.start_point, self.end_point,
self.med_custo, self.max_coust)
self.Selection_object = Selection()
self.selection = self.Selection_object.tournament
def render(self, field, key, value, REQUEST, render_prefix=None):
"""
This is where most things happens
"""
main_content = ""
here = REQUEST['here']
selection_name = field.get_value('selection_name')
default_params = field.get_value('default_params')
chart_title = field.get_value('chart_title')
data_method = field.get_value('data_method')
chart_style = field.get_value('chart_style')
x_title = field.get_value('x_title')
y_title = field.get_value('y_title')
bg_transparent = field.get_value('bg_transparent')
selection = here.portal_selections.getSelectionFor(selection_name,
REQUEST=REQUEST)
LOG(
'ZGDChart.render', 0, 'selection: %s, selection_name: %s' %
(str(selection), str(selection_name)))
# This is the default data, this is just in the case there is not method given
data = {'chart_data': []}
# Retrieve the data with the data_method
if hasattr(here, data_method):
LOG('ZGDChart.render', 0, 'found method')
data_method = getattr(here, data_method)
data['chart_data'] = data_method()
data['chart_parameter'] = {
'zgdchart_runtime_title': chart_title,
'zgdchart_runtime_xtitle': x_title,
'zgdchart_runtime_ytitle': y_title,
'zgdchart_runtime_type': 'Line_3D',
'zgdchart_runtime_bg_transparent': bg_transparent
}
# Creation selection if needed
if selection is None:
selection = Selection(selection_name, params=data)
else:
LOG('ZGDChart.render', 0, 'selection is not None')
kw = {'params': data}
selection.edit(**kw)
here.portal_selections.setSelectionFor(selection_name,
selection,
REQUEST=REQUEST)
if len(data['chart_data']) > 0:
main_content = """\
<div class="ChartContent">
<table border="0" cellpadding="0" cellspacing="0"">
<tr>
<td valign="middle" align="center" nowrap>
<img src="%s" title="Chart" border="0" alt="img"/">
</td>
</tr>
</table>
</div>""" % str(chart_style + '?selection_name=' + selection_name)
return main_content
def pushReport(self, context, render_prefix=None):
self.pushRequest()
REQUEST = get_request()
portal_selections = context.portal_selections
selection_list = [self.selection_name]
# when the Form which is specified by form_id, has a listbox, make prefixed_selection_name.
# which is based on specified selection_name in the listbox.
form_id = self.getFormId()
if form_id:
listbox = getattr(getattr(context, form_id), 'listbox', None)
if listbox is not None:
selection_name = listbox.get_value('selection_name')
if render_prefix is not None:
selection_name = '%s_%s' % (render_prefix, selection_name)
REQUEST.other['prefixed_selection_name'] = selection_name
selection_list.append(selection_name)
# save report's selection and orignal form's selection,
#as ListBox will overwrite it
for selection_name in filter(lambda x: x is not None, selection_list):
if self.temporary_selection:
portal_selections.pushSelection(selection_name)
else:
if portal_selections.getSelectionFor(selection_name) is None:
portal_selections.setSelectionFor(selection_name,
Selection(selection_name))
if self.selection_report_list is not None:
selection = portal_selections.getSelectionFor(selection_name,
REQUEST=REQUEST)
selection.edit(report_list=self.selection_report_list)
if self.selection_report_path is not None:
selection = portal_selections.getSelectionFor(selection_name,
REQUEST=REQUEST)
selection.edit(report_path=self.selection_report_path)
if self.listbox_display_mode is not None:
# XXX Dirty fix, to be able to change the display mode in form_view
REQUEST.list_selection_name = selection_name
portal_selections.setListboxDisplayMode(REQUEST,
self.listbox_display_mode,
selection_name=selection_name)
if self.selection_params is not None:
params = portal_selections.getSelectionParamsFor(selection_name,
REQUEST=REQUEST)
params.update(self.selection_params)
portal_selections.setSelectionParamsFor(selection_name,
params,
REQUEST=REQUEST)
if self.selection_columns is not None:
portal_selections.setSelectionColumns(selection_name,
self.selection_columns,
REQUEST=REQUEST)
if self.selection_sort_order is not None:
portal_selections.setSelectionSortOrder(selection_name,
self.selection_sort_order,
REQUEST=REQUEST)
if self.selection_stats is not None:
portal_selections.setSelectionStats(selection_name,
self.selection_stats,
REQUEST=REQUEST)
# When rendering a report section with a listbox, listbox gets parameters
# from request.form and edits selection with those parameters, so if you
# happen to pass explicitly selection params that have the same name as
# some request parameters (some dialog fields) but different values,
# listbox would not use your explicit parameters, but the ones from
# REQUEST.form, so we remove eventual request parameters that have the same
# name of selections parameters passed explicitly.
for selection_parameter in (self.selection_params or ()):
REQUEST.form.pop(selection_parameter, None)
class MapView( gtk.HBox ):
__pixelPerUnit = 2.5 # 2.5 means 5 pixels per Tile (a tile is two units)
def __init__( self, board, primaryObjectFamilies, secondaryObjectFamilies, primarySurfaceFamilies, secondarySurfaceFamilies ):
gtk.HBox.__init__( self, False, 0 )
self.board = board
self.board.registerView( self )
self.selection = Selection( self )
self.mouseManager = MouseManager.MouseManager( self )
for family in primaryObjectFamilies:
self.selection.addObjects( family )
for family in primarySurfaceFamilies:
self.selection.addSurfaces( family )
self.__scale = MapView.__pixelPerUnit * 4
self.__translateX = 0
self.__translateY = 0
self.__sisterViews = list()
self.drawingArea = gtk.DrawingArea()
self.drawingArea.connect( "expose-event", self.__onExposeEvent )
self.drawingArea.set_events(
gtk.gdk.EXPOSURE_MASK |
gtk.gdk.LEAVE_NOTIFY_MASK |
gtk.gdk.BUTTON_PRESS_MASK |
gtk.gdk.BUTTON_RELEASE_MASK |
gtk.gdk.POINTER_MOTION_MASK |
gtk.gdk.POINTER_MOTION_HINT_MASK
)
self.drawingArea.show()
toolBar = gtk.Toolbar()
toolBar.set_orientation( gtk.ORIENTATION_VERTICAL )
self.__objectFamilies = primaryObjectFamilies + secondaryObjectFamilies
self.__surfaces = list()
for family in secondarySurfaceFamilies + primarySurfaceFamilies:
for surface in GameItemTypes.surfaces[ family ]:
self.__surfaces.append( surface )
toolBar.append_item( _( "Select/Move" ), "", "", None, lambda widget: self.resetMouseManager() )
for family in primarySurfaceFamilies:
for surface in GameItemTypes.surfaces[ family ]:
if GameItemTypes.attributes[ surface ][ "BuiltByLengths" ]:
menu = gtk.Menu()
item = gtk.MenuItem( _( "Length" ) )
menu.append( item )
item.connect( "activate", lambda widget, surfaceType: self.mouseManager.setState( MouseManager.StartInsertSurface, surfaceType, MouseManager.SurfaceLength() ), surface )
item.show()
item = gtk.MenuItem( _( "Rectangle" ) )
menu.append( item )
item.connect( "activate", lambda widget, surfaceType: self.mouseManager.setState( MouseManager.StartInsertSurface, surfaceType, MouseManager.SurfaceRectangle() ), surface )
item.show()
toolBar.append_item( _( surface ), "", "", None, lambda widget, menu: menu.popup( None, None, None, 3, 0 ), menu )
else:
toolBar.append_item( _( surface ), "", "", None, lambda widget, surfaceType: self.mouseManager.setState( MouseManager.StartInsertSurface, surfaceType, MouseManager.SurfaceRectangle() ), surface )
for family in primaryObjectFamilies:
for category, subCategories in GameItemTypes.objects[ family ].iteritems():
menu = gtk.Menu()
for subCategory, buildingTypes in subCategories.iteritems():
for buildingType in buildingTypes:
item = gtk.MenuItem( _( buildingType ) )
menu.append( item )
item.connect( "activate", lambda widget, buildingType: self.mouseManager.setState( MouseManager.InsertingObject, buildingType ), buildingType )
if not self.board.isAvailable( buildingType ):
item.set_sensitive( False )
item.show()
toolBar.append_item( _( category ), "", "", None, lambda widget, menu: menu.popup( None, None, None, 3, 0 ), menu )
toolBar.show()
self.pack_end( toolBar, False, False, 2 )
self.pack_start( self.drawingArea, True, True, 2 )
def __onExposeEvent( self, widget, event ):
self.ctx = self.drawingArea.window.cairo_create()
self.__applyTranscale()
self.__drawboard()
self.__drawGrid()
self.mouseManager.draw()
def __drawboard( self ):
self.ctx.save()
self.ctx.set_source_rgb( 0.9, 0.9, 1 )
self.ctx.paint()
self.__drawSurfaces()
self.__drawObjects()
self.__drawSelection()
self.__drawService()
self.ctx.restore()
def __drawSurfaces( self ):
for surface in self.__surfaces:
self.__drawSurface( surface )
def __drawSurface( self, surface ):
self.__drawPolygons( self.board.getSurface( surface ).polygons, *GameItemTypes.getSurfaceColor( surface ) )
def __drawPolygons( self, polygons, r, g, b, a ):
self.ctx.save()
self.ctx.set_source_rgba( r, g, b, a )
pathPolygons( self.ctx, polygons )
self.ctx.fill()
self.ctx.restore()
def __drawObjects( self ):
for objectFamily in self.__objectFamilies:
self.__drawObjectFamily( objectFamily )
def __drawObjectFamily( self, family ):
self.ctx.save()
for o in self.board.getObjectsByFamily( family ):
self.__drawObject( o )
self.ctx.restore()
def __drawObject( self, o ):
self.drawObjectInPolygon( o.type, o.polygon, o.rotation )
if o.hasProblem:
pathPolygons( self.ctx, o.polygon.polygons )
self.ctx.set_source_rgba( 1, 0, 0, 0.5 )
self.ctx.fill()
def drawObjectInPolygon( self, resourceType, polygon, rotation ):
matrix = cairo.Matrix()
matrix.scale( MapView.__pixelPerUnit, MapView.__pixelPerUnit )
x, y = polygon.center
width, height = GameItemTypes.getObjectSize( resourceType )
matrix.translate( width, height )
matrix.rotate( -rotation * math.pi / 4 )
matrix.translate( -x, -y )
pattern = PatternRepository.getPattern( "buildings", resourceType )
pattern.set_matrix( matrix )
self.ctx.set_source( pattern )
self.ctx.paint()
def drawObjectNeeds( self, o ):
self.ctx.save()
self.ctx.set_font_size( 15 )
maxWidth = 0
self.ctx.save()
self.ctx.identity_matrix()
texts = dict()
for surface, ( needs, interaction, check ) in o.needs.iteritems():
if needs == check:
color = ( 0, 0, 0 )
elif needs:
color = ( 0.6, 0, 0 )
else:
color = ( 0, 0.5, 0 )
if needs:
needsLikes = "Needs"
else:
needsLikes = "Likes"
text = _( needsLikes + "." + surface + "." + str( interaction ) )
x_bearing, y_bearing, width, height, x_advance, y_advance = self.ctx.text_extents( text )
maxWidth = max( maxWidth, width )
texts[ text ] = color
self.ctx.restore()
x, y = o.polygon.center
self.ctx.save()
self.ctx.translate( x, y )
self.ctx.scale( 1. / self.__scale, 1. / self.__scale )
self.ctx.set_source_rgb( 1, 1, 0.6 )
self.ctx.rectangle( -5, -2, maxWidth + 10, len( texts ) * 15 + 10 )
self.ctx.identity_matrix()
self.ctx.fill_preserve()
self.ctx.set_source_rgba( 0, 0, 0, 1 )
self.ctx.stroke()
self.ctx.restore()
i = 0
for text in sorted( texts.keys() ):
i += 15
color = texts[ text ]
self.ctx.set_source_rgb( *color )
self.ctx.move_to( x, y )
self.ctx.save()
self.ctx.identity_matrix()
self.ctx.rel_move_to( 0, i )
self.ctx.show_text( text )
self.ctx.restore()
self.ctx.restore()
def __drawSelection( self ):
self.ctx.save()
pathPolygons( self.ctx, self.selection.getPolygons() )
self.ctx.identity_matrix()
self.ctx.set_source_rgb( 0, 0, 0 )
self.ctx.set_line_width( 4 )
self.ctx.stroke()
self.ctx.restore()
def __drawService( self ):
self.ctx.save()
wall = self.selection.getSurface( "Wall" ).tiles
if len( self.selection.objects ) == 1 and len( wall ) == 0:
( o, ) = self.selection.objects
if "Service.Name" in o.attributes:
self.__drawSurface( "Service." + o.attributes[ "Service.Name" ] )
if len( wall ) != 0 and len( self.selection.objects ) == 0:
self.__drawSurface( "Security" )
water = self.selection.getSurface( "Water" ).tiles
if len( water ) != 0:
self.__drawSurface( "Shoreline" )
self.ctx.restore()
def __drawGrid( self ):
self.ctx.save()
upperBound = 2 * self.board.size
self.ctx.rectangle( 0, 0, upperBound, upperBound )
if self.__scale > self.__pixelPerUnit * 2:
for i in range( 0, upperBound + 1, 2 ):
self.ctx.move_to( 0, i )
self.ctx.line_to( upperBound, i )
self.ctx.move_to( i, 0 )
self.ctx.line_to( i, upperBound )
self.ctx.set_source_rgba( 0.2, 0.2, 0.2, 0.5 )
self.ctx.identity_matrix()
self.ctx.stroke()
self.ctx.restore()
def __applyTranscale( self ):
self.ctx.scale( self.__scale, self.__scale )
self.ctx.translate( -self.__translateX, -self.__translateY )
# pixelX == self.__scale * ( logicX - self.__translateX )
# self.__scale == pixelX / ( logicX - self.__translateX )
# logicX == pixelX / self.__scale + self.__translateX
def transcalePoint( self, pixelX, pixelY ):
logicX = pixelX / self.__scale + self.__translateX
logicY = pixelY / self.__scale + self.__translateY
return logicX, logicY
def translate( self, dx, dy ):
self.__translateX -= dx / self.__scale
self.__translateY -= dy / self.__scale
self.queue_draw()
self.__transcaleSisterViews()
def zoomIn( self, x, y ):
self.__rescale( x, y, math.sqrt( 2.0 ) )
def zoomOut( self, x, y ):
self.__rescale( x, y, math.sqrt( 0.5 ) )
def __rescale( self, x, y, scale ):
oldScale = self.__scale
oldTransX = self.__translateX
oldTransY = self.__translateY
# x == oldScale * ( logicX - oldTransX )
# x == newScale * ( logicX - newTransX )
# => newScale * ( logicX - newTransX ) == oldScale * ( logicX - oldTransX )
# => logicX - newTransX == oldScale * ( logicX - oldTransX ) / newScale
# => newTransX == oldScale * ( oldTransX - logicX ) / newScale + logicX
logicX = x / self.__scale + oldTransX
logicY = y / self.__scale + oldTransY
newScale = max( self.__pixelPerUnit, oldScale * scale )
newTransX = oldScale * ( oldTransX - logicX ) / newScale + logicX
newTransY = oldScale * ( oldTransY - logicY ) / newScale + logicY
self.__scale = newScale
self.__translateX = newTransX
self.__translateY = newTransY
self.queue_draw()
self.__transcaleSisterViews()
def __transcaleSisterViews( self ):
for view in self.__sisterViews:
view.__translateX = self.__translateX
view.__translateY = self.__translateY
view.__scale = self.__scale
view.queue_draw()
def notifyView( self ):
self.queue_draw()
def resetMouseManager( self ):
self.mouseManager.reset()
self.queue_draw()
def addSisterView( self, view ):
self.__sisterViews.append( view )
class methods:
def __init__(self, fps, clockObject, surface, font, bars, windowsize):
self.fps = fps
self.clock = clockObject
self.surface = surface
self.font = font
self.bars = bars
self.windowsize = windowsize
def get_array(self, length, mode=0):
arr = list(range(length))
if not mode:
random.shuffle(arr)
elif mode == 2:
arr = arr[::-1]
elif mode == 3:
for i in range(length - 1):
if random.randint(0, 10) < 8:
tmp = random.randint(4, 15)
try:
arr[i], arr[i + tmp] = arr[i + tmp], arr[i]
except:
pass
return arr
def setup(self, length, mode=0):
self.array = self.get_array(length, mode)
self.display = Display(self.windowsize[0] / length, self.windowsize,
self.surface, self.font)
self.accesses = 0
self.comparisons = 0
setattr(self.display, "bars", self.bars)
bubble = lambda self: Bubble(self.array, self.display, self.clock, self.fps
).main()
quicksort = lambda self: Quicksort(self.array, self.display, self.clock,
self.fps).main()
selection = lambda self: Selection(self.array, self.display, self.clock,
self.fps).main()
cocktail = lambda self: Cocktail(self.array, self.display, self.clock, self
.fps).main()
bogo = lambda self: Bogo(self.array, self.display, self.clock, self.fps
).main()
oddeven = lambda self: Oddeven(self.array, self.display, self.clock, self.
fps).main()
shell = lambda self: Shell(self.array, self.display, self.clock, self.fps
).main()
comb = lambda self: Comb(self.array, self.display, self.clock, self.fps
).main()
insertion = lambda self: Insertion(self.array, self.display, self.clock,
self.fps).main()
mergetd = lambda self: MergeTD(self.array, self.display, self.clock, self.
fps).main()
radixlsd = lambda self: RadixLSD(self.array, self.display, self.clock, self
.fps).main()
counting = lambda self: Counting(self.array, self.display, self.clock, self
.fps).main()
cycle = lambda self: Cycle(self.array, self.display, self.clock, self.fps
).main()
heap = lambda self: Heap(self.array, self.display, self.clock, self.fps
).main()
circle = lambda self: Circle(self.array, self.display, self.clock, self.fps
).main()
gnome = lambda self: Gnome(self.array, self.display, self.clock, self.fps
).main()
binaryinsertion = lambda self: BinaryInsertion(
self.array, self.display, self.clock, self.fps).main()
pancake = lambda self: Pancake(self.array, self.display, self.clock, self.
fps).main()
permutation = lambda self: Permutation(self.array, self.display, self.
clock, self.fps).main()
strand = lambda self: Strand(self.array, self.display, self.clock, self.fps
).main()
bucket = lambda self: Bucket(self.array, self.display, self.clock, self.fps
).main()
minmax = lambda self: MinMax(self.array, self.display, self.clock, self.fps
).main()
mergebu = lambda self: MergeBU(self.array, self.display, self.clock, self.
fps).main()
bitonic = lambda self: Bitonic(self.array, self.display, self.clock, self.
fps).main()
stooge = lambda self: Stooge(self.array, self.display, self.clock, self.fps
).main()
smooth = lambda self: Smooth(self.array, self.display, self.clock, self.fps
).main()
quick3 = lambda self: Quick3(self.array, self.display, self.clock, self.fps
).main()
def __init__(self,
generation,
population,
limit_population,
crossover_rate,
mutation_rate,
cost_rate,
prizes_rate,
map_points,
prizes,
max_cost,
start_point,
end_point,
depositos=[]):
self.generationSize = generation
self.populationSize = population
self.limit_population = limit_population
self.crossover_rate = crossover_rate
self.mutation_rate = mutation_rate
self.cost_rate = np.array(cost_rate)
self.prizes_rate = prizes_rate
self.map_points = np.loadtxt(map_points)
self.prizes = np.loadtxt(prizes)[:, 1]
self.max_cost = np.array(max_cost)
self.start_point = start_point
self.end_point = end_point
self.depositos = depositos
self.number_agents = len(max_cost)
self.distance = self.calculate_distances()
self.functionObject = FunctionObjective(self.map_points, self.prizes)
self.FO = self.functionObject.FO
self.mensureCost = self.functionObject.med_custo
self.methodInsertRemoveChromosome = self.functionObject.coust_insert
self.allElementsMap = np.arange(self.map_points.shape[0])
self.allElementsMap = self.allElementsMap[self.number_agents:]
# removendo depositos
deposits = [x for x in self.start_point]
deposits += [x for x in self.end_point if x not in deposits]
deposits = np.unique(np.array(deposits))
self.initialChromossome = np.arange(self.map_points.shape[0])
self.initialChromossome = np.delete(self.initialChromossome,
self.depositos)
self.allElementsMap = np.copy(self.initialChromossome)
self.mutationObject = Mutation(self.mensureCost, self.max_cost,
self.prizes)
self.mutation = self.mutationObject.scramble
self.crossoverObject = Crossover()
self.crossover = self.crossoverObject.cross_TOPMD
self.PopulationObject = Population(self.start_point, self.end_point,
self.mensureCost, self.max_cost,
self.distance)
self.SelectionObject = Selection()
self.selection = self.SelectionObject.tournament