def generarorbes(self):
index = self.buscarcapa("Orbeski")
if index > -1:
for i in self.datos["layers"][index]["objects"]:
pos = (i["x"], i["y"])
orb = comp.Orbes("Ki", pos)
c.Grupos["orbes"].add(orb)
c.Grupos["todos"].add(orb)
for i in self.datos["layers"][index + 1]["objects"]:
pos = (i["x"], i["y"])
orb = comp.Orbes("Vida", pos)
c.Grupos["orbes"].add(orb)
c.Grupos["todos"].add(orb)
for i in self.datos["layers"][index + 2]["objects"]:
pos = (i["x"], i["y"])
orb = comp.Orbes("Trampa", pos)
c.Grupos["orbes"].add(orb)
c.Grupos["todos"].add(orb)
for i in self.datos["layers"][index + 3]["objects"]:
pos = (i["x"], i["y"])
orb = comp.Orbes("Exp", pos)
c.Grupos["orbes"].add(orb)
c.Grupos["todos"].add(orb)
else:
print "No se generaron orbes"
def _build_tree_static(self, proc_mat, fraction, parent_id, idx_map):
""" Recursive top-down (start at root) construction
of a tree. This construction is static, i.e. it
is built from the same processed pair-wise matrix,
the relationships do not change based on the level
of the tree.
"""
if fraction < 0:
return
c = Components(proc_mat)
components = c.get_components(fraction, proc_mat)[0]
for component in components:
i_map = idx_map[component]
b_mat = self.base_affinity_matrix[i_map,:][:,i_map]
p_mat = self.proc_affinity_matrix[i_map,:][:,i_map]
keys = self.key_list[i_map]
n_id = len(self.nodes)
n = Node(i_map, keys, b_mat, p_mat, n_id)
n._parent = parent_id
if parent_id is not None:
self.nodes[parent_id]._children.append(n_id)
self.nodes[n_id] = n
fraction = fraction - 1/float(self.fixed_k)
self._build_tree_static(p_mat, fraction, n_id, i_map)
def make_transmitter_boxes(self):
y_coord = 0 + Config.wall_padding
x_start = 0 + Config.wall_padding
i = 0
for x_coord in Utils.frange(
x_start,
Config.wall_padding + (num_of_packets * Config.packet_width) +
(num_of_packets * Config.packet_padding),
Config.packet_padding + Config.packet_width):
# First make the border for the packet
border = Components.Box(
x_coord - Config.border_width, y_coord - Config.border_width,
Config.packet_width + 2 * Config.border_width,
Config.packet_height + 2 * Config.border_width,
Config.border_color)
self.border_sprite_list.add(border)
# Make the transmitter box
new_transbox = Components.TransmitterBox(x_coord, y_coord)
self.transmitter_list.add(new_transbox)
self.transmitter_map[i] = new_transbox
# Make the packet (with it's coordinates the same as the transmitter box)
new_packet = Components.Packet(x_coord, y_coord)
self.packet_list.add(new_packet)
self.packet_map[i] = new_packet
i += 1
def makeboot(self):
c.LevelTutorial["TeclasMovimiento"].convert_alpha()
self.tuto = {
"Teclas": True,
"Espacio": False,
"Orbes": False,
"Busca": False,
"Pelea": False
}
self.listaenemigos = {"Triceratops": False, "Generador": True}
self.target = [None]
self.listname = ["Espacio", "Orbes", "Busca", "Pelea"]
self.bg = comp.Background(self.tamano_mundo,
c.LevelTutorial["Background"])
self.goku = comp.Goku(self.tamano_mundo, self.target)
self.goku.rect.x = 320
self.goku.rect.y = 512
self.krilin = comp.Ciudadano((320, 512), 0)
c.Grupos["usuarios"].add(self.goku)
#Anadir objetos GRUPO TODOS
self.generarmuros(self.listname)
c.Grupos["todos"].add(self.bg)
self.generarorbes()
self.generarenemigos(self.listaenemigos)
c.Grupos["todos"].add(self.krilin)
c.Grupos["todos"].add(self.goku)
self.generarforeground()
def make_receiver_boxes(self):
y_coord = Config.window_height - Config.wall_padding - Config.packet_height
x_start = 0 + Config.wall_padding
i = 0
for x_coord in Utils.frange(
x_start,
Config.wall_padding + (num_of_packets * Config.packet_width) +
(num_of_packets * Config.packet_padding),
Config.packet_padding + Config.packet_width):
# First make the border for the packet
border = Components.Box(
x_coord - Config.border_width, y_coord - Config.border_width,
Config.packet_width + 2 * Config.border_width,
Config.packet_height + 2 * Config.border_width,
Config.border_color)
self.border_sprite_list.add(border)
# Make the new receiver box
new_recbox = Components.ReceiverBox(x_coord, y_coord)
self.receiver_list.add(new_recbox)
self.receiver_map[i] = new_recbox
# Make the ACK packet (with it's coordinates the same as the receiver box)
ack_packet = Components.AckPacket(x_coord, y_coord)
self.ack_list.add(ack_packet)
self.ack_map[i] = ack_packet
i += 1
def _construct_CNN_input(self, input_model, p_size, kernels):
# CNN input block
model = cmp.Conv1D_input_layer(input_model,
self.CNN_sizes[p_size[0]],
kernel_shape=kernels[0])
# CNN Res Block
min_1 = (self.CNN_sizes[p_size[1]] -
1) if (self.CNN_sizes[p_size[1]] - 1) > -1 else 0
filters_res = [min_1, min_1, self.CNN_sizes[p_size[1]]]
model = cmp.Conv1D_res_block(model,
n_filters=filters_res,
kernel_shape=kernels[1])
# Dropout
model = self._add_dropout(model, DNN=False)
# CNN Identity Block
filters_id = [self.CNN_sizes[p_size[2]], self.CNN_sizes[p_size[1]]]
model = cmp.Conv1D_identity_block(model,
filters_id,
kernel_shape=kernels[2])
# Dropout
model = self._add_dropout(model, DNN=False)
return model
def GetMacCabeMetric(path):
"""
"""
complexity = 0.0
try:
p = os.path.dirname(path)
if p not in sys.path:
sys.path.append(p)
import maccabe as codepaths
except ImportError as info:
msg = 'ERROR: maccabe module not imported: %s\n' % info
sys.stderr.write(msg)
return complexity
else:
cls = Components.GetClass(path)
if inspect.isclass(cls):
args = Components.GetArgs(cls)
devs = getInstance(cls, args)
### Get class of model
if not path.endswith('.pyc'):
### mcCabe complexity
### beware to use tab for devs code of models
L = [
getattr(cls, fct)
for fct in ('extTransition', 'intTransition', 'outputFnc')
if hasattr(cls, fct)
]
source_list = list(map(inspect.getsource, L))
L_args = []
for text in source_list:
### textwrap for deleting the indentation
ast = codepaths.ast.parse(textwrap.dedent(text).strip())
visitor = codepaths.PathGraphingAstVisitor()
visitor.preorder(ast, visitor)
for graph in visitor.graphs.values():
complexity += graph.complexity()
return complexity
### for .pyc file
else:
return 0.0
else:
return 0.0
def generarforeground(self):
index = self.buscarcapa("Palmeras")
if index > -1:
for i in self.datos["layers"][index]["objects"]:
pos = (i["x"], i["y"] - i["height"])
m = comp.Palmera(pos)
c.Grupos["todos"].add(m)
for i in self.datos["layers"][index + 1]["objects"]:
pos = (i["x"], i["y"] - i["height"])
m = comp.Edificio(pos)
c.Grupos["todos"].add(m)
else:
print "No se genero foreground"
def _construct_CNN(self, input_, p_size, params):
# Input block
k_size = [
params["k_size_input"], params["k_size_b1"], params["k_size_b2"],
params["k_size_b3"]
]
model = self._construct_CNN_input(input_, p_size, k_size)
# Block 3 res
min_3 = (self.CNN_sizes[p_size[3]] -
1) if (self.CNN_sizes[p_size[3]] - 1) > -1 else 0
filters_res = [min_3, min_3, self.CNN_sizes[p_size[3]]]
model = cmp.Conv1D_res_block(model, filters_res, k_size[3])
# Dropout
model = self._add_dropout(model, DNN=False)
# Extra blocks, gotta get deep
model = cmp.Conv1D_res_block(model, [128, 128, 128], kernel_shape=3)
# Dropout
model = self._add_dropout(model, DNN=False)
model = cmp.Conv1D_res_block(model,
[128, 128, self.CNN_sizes[p_size[3]]],
kernel_shape=3)
# Dropout
model = self._add_dropout(model, DNN=False)
if params["type_b4"] == 0:
# Block 4 ID
filters_id = [self.CNN_sizes[p_size[4]], self.CNN_sizes[p_size[3]]]
model = cmp.Conv1D_identity_block(model,
filters_id,
kernel_shape=3)
# Dropout
model = self._add_dropout(model, DNN=False)
# Flatten for dense
model = kl.Flatten()(model)
else:
# Flatten for dense
model = kl.Flatten()(model)
# Dense ID Block 4
model = cmp.dense_res_block(model, self.DNN_sizes[p_size[4]])
# Dropout
model = self._add_dropout(model, DNN=True)
return model
def set_program(self, event):
""" Kick off spacecraft info reading and display script names in windows
Description: Creates Reader and Writer objects, commencing reading of inputs. Then displays script names.
"""
# Clear output
self.out_text.config(state=tkinter.NORMAL)
self.out_text.delete(1.0,self.output_text_len+1.0)
self.out_text.config(state=tkinter.DISABLED)
# Clear listboxes
self.a_htr_display.delete(0, len(self.ah_scripts))
self.cf_htr_display.delete(0, len(self.cfh_scripts))
self.twta_display.delete(0, len(self.twta_scripts))
# Create spacecraft
self.spacecraft = Components.Spacecraft()
self.spacecraft.name = self.program_combo.get()
self.spacecraft.script_dir = self.programs[self.spacecraft.name][0]
self.spacecraft.data_dir = self.programs[self.spacecraft.name][1]
self.spacecraft.db_dir = self.programs[self.spacecraft.name][2]
self.author = self.author_text.get()
# Create I/O objects
try:
self.reader = IOUtils.Reader(gui=self, spacecraft=self.spacecraft)
self.reader.execute()
self.writer = IOUtils.Writer(gui=self, dbase=self.reader.dbase, spacecraft=self.spacecraft, author=self.author)
self.output_text('')
except Exception as error:
self.output_text('Failed to read spacecraft info: %s' % error)
out = traceback.format_exc()
self.output_text(out)
print(out)
def __init__(self, in_channels, out_channels):
super(cSAWGANGeneratorV1, self).__init__()
# (N, in_channels, 1, 1)
self.l1 = nn.Sequential(
nn.utils.spectral_norm(nn.ConvTranspose2d(in_channels=in_channels, out_channels=1024, kernel_size=4, stride=1, padding=0)),
nn.BatchNorm2d(num_features=1024),
nn.LeakyReLU(0.1)
)
# (N, 1024, 4, 4)
self.l2 = nn.Sequential(
nn.utils.spectral_norm(nn.ConvTranspose2d(in_channels=1024, out_channels=512, kernel_size=4, stride=2, padding=1)),
nn.BatchNorm2d(num_features=512),
nn.LeakyReLU(0.1)
)
# (N, 512, 8, 8)
self.l3 = nn.Sequential(
nn.utils.spectral_norm(nn.ConvTranspose2d(in_channels=512, out_channels=256, kernel_size=4, stride=2, padding=1)),
nn.BatchNorm2d(num_features=256),
nn.LeakyReLU(0.1)
)
self.attn = Components.SelfAttention(in_channels=256)
# (N, 256, 16, 16)
self.l4 = nn.Sequential(
nn.utils.spectral_norm(nn.ConvTranspose2d(in_channels=256, out_channels=out_channels, kernel_size=4, stride=2, padding=1)),
nn.Tanh()
)
def _construct_DNN(self, input_, p_size):
# Input blocks
model = self._construct_DNN_input(input_, p_size)
# Block 3 Dense Res
model = cmp.dense_res_block(model, self.DNN_sizes[p_size[3]])
model = self._add_dropout(model, DNN=True)
# Block 4 Dense ID
model = cmp.dense_identityblock(model, self.DNN_sizes[p_size[4]],
self.DNN_sizes[p_size[3]])
# Dropout
model = self._add_dropout(model, DNN=True)
return model
async def __worker(self, json_request):
try:
workflow_index = json_request["workflow_index"]
item = json_request["item"]
item_type = item["item_type"]
item_name = item["item_name"]
video = item.get("video", None)
rules = item.get("rules", None)
except KeyError as e:
raise ServiceException(
reason=f'Field {e} is missing in the payload.',
status_code=400)
meta_data = {"video": video, "rules": rules}
workflow = self.workflow_lookup[workflow_index]
item = Components.item_factory(item_type=item_type,
item_name=item_name,
item_step=None,
**meta_data)
item_index = len(self.item_lookup.keys())
self.item_lookup[item_index] = item
workflow.add_item(item)
res = {
"item_index":
item_index,
"message":
f"Item {item.item_name} was added successfully to workflow of index {workflow_index}. "
f"Item is now accessible at index {item_index}",
"workflow":
str(workflow)
}
return json.dumps(res)
def __init__(self, pid, loc, dir):
self.colliding = False
self.image = pygame.Surface(
[v.bullet_scale * v.cell_size, v.bullet_scale * v.cell_size])
self.image.fill(pygame.Color(80, 50, 156, 255))
self.velocity = Components.Velocity(dir * v.bullet_speed, 0, pid)
Entity.__init__(self, pid, loc[0], loc[1])
def paint_plane(self):
self.big_jet_plane = Components.BigJetPlane(self)
self.add(self.big_jet_plane,
(WINDOW_WIDTH - Components.BigJetPlane.TEST_SIZE) / 2,
(WINDOW_HEIGHT - Components.BigJetPlane.TEST_SIZE))
self.addEventListener("click", self.click_listener)
self.addEventListener("mousemove", self.big_jet_plane.move_listener)
def generarenemigos(self, listaenemigos):
index = self.buscarcapa("Triceratops")
if index > -1:
if listaenemigos["Triceratops"]:
for i in self.datos["layers"][index]["objects"]:
pos = (i["x"], i["y"])
en = comp.Triceratops(pos, self.target)
c.Grupos["enemigos"].add(en)
c.Grupos["todos"].add(en)
if listaenemigos["Generador"]:
for i in self.datos["layers"][index + 1]["objects"]:
pos = (i["x"], i["y"])
en = comp.GeneradorMinions(pos, self.target)
#c.Grupos["enemigos"].add(en)
c.Grupos["todos"].add(en)
else:
print "No se generaron enemigos"
def _build_tree_dynamic(self):
""" Non-recursive bottom-up construction of the tree;
at each level the pair-wise relationships are updated
between components - where the instances inside components
influence each others relationship to instances in other
components
"""
node_id = 0
fractions = dice_fractions(self.fixed_k)
c = Components(self.proc_affinity_matrix)
#Build the bottom level
components, comp_mat = c.get_components(fractions.next(),
self.proc_affinity_matrix,
strongly_connected=True)
for component in components:
base_mat = self.base_affinity_matrix[component,:][:,component]
proc_mat = self.proc_affinity_matrix[component,:][:,component]
keys = self.key_list[component]
n = Node(component, keys, base_mat, proc_mat, node_id)
self.nodes[node_id] = n
node_id += 1
node_offset = temp_offset = 0
for fraction in fractions:
temp_offset += len(components)
c = Components(comp_mat)
components, comp_mat = c.get_components(fraction, comp_mat, True)
for component in components:
instances = []
for instance in component:
idx = instance + node_offset
self.nodes[idx]._parent = node_id
instances += self.nodes[idx].list_of_instances
base_mat = self.base_affinity_matrix[instances,:][:,instances]
proc_mat = self.proc_affinity_matrix[instances,:][:,instances]
keys = self.key_list[instances]
n = Node(instances, keys, base_mat, proc_mat, node_id)
n._children = list(asanyarray(component) + node_offset)
self.nodes[node_id] = n
node_id += 1
node_offset = temp_offset
self.root_id = node_id - 1
def initUI(self, name, parent, tracker):
#parsePlantXML(name)
#FOR TESTING PURPOSES ONLY!!!!!
lastDigit = name[-1]
componentList = ["M-"+lastDigit+"-1","M-"+lastDigit+"-2","M-"+lastDigit+"-3",
"T-"+lastDigit+"-1","T-"+lastDigit+"-2","T-"+lastDigit+"-3",
"M-"+lastDigit+"-4","M-"+lastDigit+"-5","M-"+lastDigit+"-6"]
grid = QtGui.QGridLayout()
upperPartLayout = QtGui.QHBoxLayout()
grid.setSpacing(10)
grid.setVerticalSpacing(20)
#floorList is returned by xml parser --> ["Floor 1","Floor 2",...]
#create instances of FloorButton (extends AbstractButton) from floorList
for i in range(len(componentList)):
theComponent = Components(componentList[i],self,self.tracker) #should be Component
theComponentButton = ComponentButton(componentList[i],self,theComponent)
theComponent.addButton(theComponentButton)
self.componentButtonList.append(theComponentButton) #was GtGui.QPushButton
#uncomment when ComponentButton is written!!!!!!!!!!!!!!!!!!!!!!1
#self.roomButtonList.append(RoomButton(roomList[i], self, theRoom)) #abstract button --> FloorButton
self.componentObjectList.append(theComponent)
theComponent.addToFinalComponentList()
for k in range(len(self.componentButtonList)):
upperPartLayout.addWidget(self.componentButtonList[k])
grid.addLayout(upperPartLayout, 0,0,1,2)
grid.addWidget(self.componentObjectList[k], 1, 0)
test = QtGui.QGroupBox('test',self)
test.setStyleSheet("""QGroupBox { border: 2px solid rgb(0, 34, 102); background-color: rgb(0, 34, 102);
border-radius: 6px; padding-top: 20px; }""")
grid.addWidget(test,1,1)
# for k in range(len(self.floorObjectList)):
# grid.addWidget(self.floorObjectList[k], 1, 0, 1, len(self.floorButtonList))
self.setLayout(grid)
self.setStyleSheet(""".Room { background-color: rgb(255, 255, 255); font-size: 10px; border-radius: 6px; }
.Room::title { color: transparent; background-color: transparent; padding-top: 5px; padding-left: 5px;}""")
def _construct_DNN_input(self, input_model, p_size):
# Input
model = cmp.dense_simple_layer(input_model, self.DNN_sizes[p_size[0]])
# Dense Res Block
model = cmp.dense_res_block(model, self.DNN_sizes[p_size[1]])
# Dropout
model = self._add_dropout(model)
# Dense Identity Block
model = cmp.dense_identityblock(model, self.DNN_sizes[p_size[2]],
self.DNN_sizes[p_size[1]])
# Dropout
model = self._add_dropout(model)
return model
def AddObject():
global listDraw
global listPlatformCollider
global listEnemy
# add the ground
ground = COMP.GameObject()
ground.SetSolid(RED,800,300)
ground.rect.y = 500
# Create enemy.
Info2 = COMP.GameObject()
Info2.SetSprite(alien)
Info2.objectName = "alien"
Info2.SetLocation([750,410])
listDraw.add(ground)
listDraw.add(Info2)
listPlatformCollider.add(ground)
listEnemy.append(Info2)
def makeboot(self):
self.listaenemigos = {"Triceratops": False, "Generador": True}
self.target = [None]
comp.Global_posicion_x = -256
comp.Global_posicion_y = -335
self.misiones = ["Derrota a Cell"]
self.bg = comp.Background(self.tamano_mundo,
c.LevelFinalGraficos["Background"])
self.goku = comp.Goku(self.tamano_mundo, self.target)
self.goku.rect.x = 100
self.goku.rect.y = 512
c.Grupos["usuarios"].add(self.goku)
#Anadir objetos GRUPO TODOS
self.generarmuros()
c.Grupos["todos"].add(self.bg)
#self.generarorbes()
#self.generarenemigos(self.listaenemigos)
c.Grupos["todos"].add(self.goku)
def generarmuros(self, listname=None):
index = self.buscarcapa("Muros")
print index
if index > -1:
for i in self.datos["layers"][index]["objects"]:
possize = (i["x"], i["y"], i["width"], i["height"])
m = comp.Muro(possize)
c.Grupos["muros"].add(m)
c.Grupos["todos"].add(m)
if listname != None:
j = 0
for i in self.datos["layers"][index + 1]["objects"]:
possize = (i["x"], i["y"], i["width"], i["height"])
m = comp.CollisionChecker(possize)
m.name = listname[j]
j += 1
c.Grupos["collisions"].add(m)
c.Grupos["todos"].add(m)
else:
print "No se generaron muros"
def OnItemDeselected(self, event):
""" Item has been deselected
"""
line_number = self.getColumnText(self.currentItem, 2)
python_path = self.getColumnText(self.currentItem, 4)
if line_number != "":
### DEVS model retrieve
devs = getInstance(Components.GetClass(python_path))
### check error and change image
if not isinstance(devs, tuple):
self.SetItemImage(self.currentItem, self.idx2)
def AddEnemy(enemy):
Info2 = COMP.GameObject()
if(enemy == 5):
Info2.SetSprite(flyingAlien)
Info2.SetLocation([750, 215])
else:
Info2 .SetSprite(alien)
Info2.SetLocation([750, 410])
Info2.objectName = "alien"
listDraw.add(Info2)
listEnemy.append(Info2)
def Save(self, obj_dumped, fileName=None):
""" Function that save the codeblock on the disk.
"""
assert (fileName.endswith(tuple(DumpZipFile.ext)))
### local copy of paths
python_path = obj_dumped.python_path
image_path = obj_dumped.image_path
### Now, file paths are in the compressed file
if os.path.isabs(python_path):
obj_dumped.python_path = os.path.join(
fileName, os.path.basename(obj_dumped.python_path))
if os.path.isabs(image_path):
obj_dumped.image_path = os.path.join(
fileName, os.path.basename(obj_dumped.image_path))
obj_dumped.model_path = fileName
### args is constructor args and we save these and not the current value
if hasattr(obj_dumped, 'args'):
obj_dumped.args = Components.GetArgs(
Components.GetClass(obj_dumped.python_path))
try:
fn = 'DEVSimPyModel.dat'
### dump attributes in fn file
cPickle.dump(obj=PickledCollection(obj_dumped),
file=open(fn, "wb"),
protocol=0)
except Exception, info:
sys.stderr.write(
_("Problem saving (during the dump): %s -- %s\n") %
(str(fileName), info))
return False
def __init__(self, parent, id, model=None):
wx.Choicebook.__init__(self, parent, id)
self.parent = parent
cls = Components.GetClass(model.python_path)
if inspect.isclass(cls):
pageTexts = {
_('Doc'):
inspect.getdoc(cls),
_('Class'):
inspect.getsource(cls),
_('Constructor'):
inspect.getsource(cls.__init__),
_('Internal Transition'):
inspect.getsource(cls.intTransition),
_('External Transition'):
inspect.getsource(cls.extTransition),
_('Output Function'):
inspect.getsource(cls.outputFnc),
_('Time Advance Function'):
inspect.getsource(cls.timeAdvance),
_('Finish Function'):
inspect.getsource(cls.finish)
if hasattr(cls, 'finish') else "\tpass"
}
else:
pageTexts = {
_("Importing Error"):
_("Error trying to import the module: %s.\nChange the python path by clicking in the above 'python_path' cell.\n %s"
% (model.python_path, str(cls)))
}
# Now make a bunch of panels for the choice book
for nameFunc in pageTexts:
win = wx.Panel(self)
box = wx.BoxSizer(wx.HORIZONTAL)
st = wx.TextCtrl(win, wx.NewId(), '', style=wx.TE_MULTILINE)
try:
txt = unicode(pageTexts[nameFunc],
errors='replace').encode('utf-8')
except TypeError:
txt = pageTexts[nameFunc]
st.AppendText(txt)
st.ShowPosition(wx.TOP)
st.SetEditable(False)
box.Add(st, 1, wx.EXPAND)
win.SetSizer(box)
self.AddPage(win, nameFunc)
def __init__(self,
x,
y,
char,
name,
color,
speed=10,
blocks=False,
blocks_sight=False,
delay=0,
fighter=None,
always_visible=False,
ai=None,
item=None,
equipment=None,
ranged=None):
self.name = name
self.blocks = blocks
self.blocks_sight = blocks_sight
self.x = x
self.y = y
self.delay = delay
self.base_speed = speed
self.char = char
self.color = Color(color)
self.always_visible = always_visible
self.path = None
self.status = Status.StatusList()
# Optional Components
self.fighter = fighter
if self.fighter: # let the fighter component know who owns it
self.fighter.owner = self
self.ranged = ranged
if self.ranged: # let the fighter component know who owns it
self.ranged.owner = self
self.ai = ai
if self.ai: # let the AI component know who owns it
self.ai.owner = self
self.item = item
if self.item: # let the Item component know who owns it
self.item.owner = self
self.equipment = equipment
if self.equipment: # let the Equipment component know who owns it
self.equipment.owner = self
self.item = Components.Item()
self.item.owner = self
def getComponents( matches, max_distance = 0, min_overlap = 0, by_query = False ):
"""return overlapping matches.
max_distance
allow reads to be joined if they are # residues apart.
Adjacent reads are 1 residue apart, overlapping reads are 0 residues
apart
min_overlap
require at least # residues to be overlapping
"""
addAlignments( matches, by_query = by_query )
components = Components.IComponents()
for x in range(0, len(matches)):
components.add( x, x)
if min_overlap > 0 and max_distance > 0:
raise ValueError( "both min_overlap (%i) and max_distance (%i) > 0" % (min_overlap, max_distance) )
if by_query:
if min_overlap > 0:
f = lambda x,y: alignlib_lite.py_getAlignmentOverlap( \
matches[x].mMapQuery2Target,
matches[y].mMapQuery2Target,
alignlib_lite.py_RR ) >= min_overlap
else:
f = lambda x,y: alignlib_lite.py_getAlignmentShortestDistance( \
matches[x].mMapQuery2Target,
matches[y].mMapQuery2Target,
alignlib_lite.py_RR ) <= max_distance
else:
if min_overlap > 0:
f = lambda x,y: alignlib_lite.py_getAlignmentOverlap( \
matches[x].mMapTarget2Query,
matches[y].mMapTarget2Query,
alignlib_lite.py_RR ) >= min_overlap
else:
f = lambda x,y: alignlib_lite.py_getAlignmentShortestDistance( \
matches[x].mMapTarget2Query,
matches[y].mMapTarget2Query,
alignlib_lite.py_RR ) <= max_distance
for x in range(len(matches)):
for y in range(0, x):
if f(x,y): components.add( x, y )
return components.getComponents()
def computeMW(mol):
"""mol -> mw of largest fragment, mw of total molecule"""
fragments = []
total = 0.0
if not mol.atoms: return 0.0, 0.0
for atoms, bonds in Components.components(mol):
mw = 0.0
for atom in atoms:
mw += atom.mass + atom.hcount
fragments.append(mw)
total += mw
largest = max(fragments)
return largest, total
def applyMethod(self):
"""index the graph.
"""
componentor = Components.SComponents()
infile = open(self.mFilenameAlignments, "r")
naccepted, nrejected_score, nrejected_aligned = 0, 0, 0
for line in infile:
if line[0] == "#": continue
if line.startswith("passed"): continue
(qdomain, sdomain, estimate, code,
qstart, qend, qali, sstart, send, sali,
score, naligned, ngaps, zscore) =\
line[:-1].split("\t")
if code == "+":
if int(naligned) >= self.mMinAlignedResidues:
componentor.add(qdomain, sdomain)
naccepted += 1
else:
nrejected_aligned += 1
nrejected_score += 1
self.info( "computing components with %i accepted links (%i rejected score, %i rejected alignment length)" %\
(naccepted, nrejected_score, nrejected_aligned ) )
components = componentor.getComponents()
self.mOutfile.write("nid\tstart\tend\tfamily\n")
noutput = 0
family_id = 0
nids = set()
for domains in components:
family_id += 1
for domain in domains:
nid, start, end = domain.split("_")
nids.add(nid)
self.mOutfile.write( "%s\t%s\t%s\t%s\n" % \
( nid, start, end, self.mPatternFamily % family_id ) )
noutput += 1
self.info("output from mst: nsequences=%i, nclusters=%i, ndomains=%i" %
(len(nids), family_id, noutput))
self.mOutfile.close()
def makeboot(self):
self.listaenemigos = {"Triceratops": True, "Generador": True}
self.target = [None]
self.framescont = 0
self.sec = 59
self.min = 1
self.timecount = False
self.mision1 = False
self.and17 = False
self.androide17 = None
self.misiones = [
"Salava a Bulma y a Milk", "El tiempo se agota!!, sube tu nivel"
]
self.bg = comp.Background(self.tamano_mundo,
c.Level1Graficos["Background"])
self.goku = comp.Goku(self.tamano_mundo, self.target)
self.goku.rect.x = 100
self.goku.rect.y = 512
self.bulma = comp.Ciudadano((1946, 1396), 1)
self.milk = comp.Ciudadano((1908, 3295), 2)
c.Grupos["ciudadanos"].add(self.bulma)
c.Grupos["ciudadanos"].add(self.milk)
c.Grupos["usuarios"].add(self.goku)
#Anadir objetos GRUPO TODOS
self.generarmuros()
c.Grupos["todos"].add(self.bg)
self.generarorbes()
self.generarenemigos(self.listaenemigos)
c.Grupos["todos"].add(self.bulma)
c.Grupos["todos"].add(self.milk)
c.Grupos["todos"].add(self.goku)
self.generarforeground()
def OnDoubleClick(self, event):
""" Double click on cell has been invocked
"""
line_number = self.getColumnText(self.currentItem, 2)
python_path = self.getColumnText(self.currentItem, 4)
if line_number != "":
devscomp = Components.DEVSComponent()
devscomp.setDEVSPythonPath(python_path)
editor_frame = Components.DEVSComponent.OnEditor(devscomp, event)
if editor_frame:
editor_frame.text.GotoLine(int(line_number))
event.Skip()
def __init__(self, in_channels, num_classes):
super(cSAWGANDiscriminatorV1, self).__init__()
# (N, in_channels, 32, 32)
self.l1 = nn.Sequential(
nn.utils.spectral_norm(
nn.Conv2d(in_channels=in_channels,
out_channels=256,
kernel_size=4,
stride=2,
padding=1)), nn.BatchNorm2d(num_features=256),
nn.LeakyReLU(0.2))
self.attn = Components.SelfAttention(in_channels=256)
# (N, 256, 16, 16)
self.l2 = nn.Sequential(
nn.utils.spectral_norm(
nn.Conv2d(in_channels=256,
out_channels=512,
kernel_size=4,
stride=2,
padding=1)), nn.BatchNorm2d(num_features=512),
nn.LeakyReLU(0.2))
# (N, 512, 32, 32)
self.l3 = nn.Sequential(
nn.utils.spectral_norm(
nn.Conv2d(in_channels=512,
out_channels=1024,
kernel_size=4,
stride=2,
padding=1)), nn.BatchNorm2d(num_features=1024),
nn.LeakyReLU(0.2))
# (N, 1024, 4, 4)
self.l4 = nn.Sequential(
nn.utils.spectral_norm(
nn.Conv2d(in_channels=1024,
out_channels=1024,
kernel_size=4,
stride=1,
padding=0)), nn.BatchNorm2d(num_features=1024),
nn.LeakyReLU(0.2))
# (N, 1024, 1, 1)
self.l5 = nn.Sequential(
nn.utils.spectral_norm(
nn.Linear(in_features=1024 + num_classes, out_features=1)))
#cost_mat = genfromtxt(data_path + '/cost-matrices/' + sys.argv[1])
""" Compute the bullseye score.
Assuming MPEG-7 data is loaded
"""
e = Evaluation(cost_mat, 20, 70)
print "Top 40 bullseye score: ", e.bullseye(40)
""" Compute a new similarity matrix using dice coefficient
as a population cue
"""
#Geometric mean, to ensure symmetry
cost_mat = sqrt(cost_mat * cost_mat.transpose())
p = Population(cost_mat, 20, 70, verbose=True)
#Not setting k will attempt to automatically find it!
processed_matrix = p.generate_diff(k=13)
e = Evaluation(processed_matrix, 20, 70)
print "Top 40 bullseye score using dice: ", e.bullseye(40)
""" Update the similarity matrix further using the previous
matrix to build components
"""
c = Components(processed_matrix)
c.get_components(0.3, strongly_connected=False)
comp_mat = c._expand_component_difference()
e = Evaluation(comp_mat, 20, 70)
print "Top 40 bullseye score after components: ", e.bullseye(40)