def main():
# creates cells to build lists
a = cell.Cell(4)
b = cell.Cell(3, a)
c = cell.Cell(2, b)
d = cell.Cell(1, c)
e = cell.Cell(9)
f = cell.Cell(8, e)
g = cell.Cell(7, f)
h = cell.Cell(6, g)
i = cell.Cell(5, h)
z = cell.Cell(0)
# prints list A
A = linkedList.LinkedList(d)
print "list A:"
A.echo()
# prints list B
B = linkedList.LinkedList(i)
print "list B:"
B.echo()
# prints the concatenated list
X = list_concat(A, B)
print "concatenation:"
X.echo()
def test_find_occurence(self):
'''Test how long a basic function takes.'''
tries = 1000
print 'Time per operation: find_occurences (average over {0} tries):\n'.format(tries)
sequences = [';' + 'AG' * 10 + ';',
';' + 'AG' * 500 + ';']
for sequence in sequences:
c = cell.Cell(sequence)
before = time.time()
for i in range(tries):
c.find_occurences('own', 0, len(sequence), 'AGA', 1000)
time_passed = 1000 * (time.time() - before)/tries
print 'Normal: Length sequence: {0}, Time/Action: {1} ms'.format(len(sequence), time_passed)
prom_sequences = [';' + 'PAGAC' * 5 + ';',
';' + 'PAGAC' * 190 + ';']
for sequence in prom_sequences:
c = cell.Cell(sequence)
before = time.time()
for i in range(tries):
c.find_occurences('prom', 0, len(sequence), 'AGA', 1000)
time_passed = 1000 * (time.time() - before)/tries
print 'Promoter: Length sequence: {0}, Time/Action: {1} ms'.format(len(sequence), time_passed)
time.sleep(0.1)
def __init__(self, height, width, mines):
self.height = height
self.width = width
self.mines = mines
self.minesLoc = []
self.marks = []
self.totalCells = width * height
self.uncovered = 0
# Mines locations generation
minesUsed = 0
while (minesUsed < mines):
rdR = rd.randint(0, height - 1)
rdC = rd.randint(0, width - 1)
mineLoc = str(rdR) + ',' + str(rdC)
if mineLoc not in self.minesLoc:
self.minesLoc.append(mineLoc)
minesUsed = minesUsed + 1
# Board filling
self.board = [[cell.Cell() for r in range(width)]
for c in range(height)]
for i in range(len(self.minesLoc)):
pos = self.minesLoc[i].split(',')
row = int(pos[0])
col = int(pos[1])
self.board[row][col] = cell.Cell(True)
self.seekMines()
def test_prob1(length):
start = cell.Cell(20)
next_c = start
# creates a cell list of size length
for i in (range(1, length)):
new_c = cell.Cell(random.randint(1, length))
# add new_cell to list
list_concat(next_c, new_c)
# move to next cell
next_c = new_c
def main():
# creates cells to build lists
a = cell.Cell(4)
b = cell.Cell(3, a)
c = cell.Cell(2, b)
d = cell.Cell(1, c)
e = cell.Cell(9)
f = cell.Cell(8, e)
g = cell.Cell(7, f)
h = cell.Cell(6, g)
i = cell.Cell(5, h)
# prints list A
A = linkedList.LinkedList(d)
print "list A:"
A.echo()
# prints list B
B = linkedList.LinkedList(i)
print "list B:"
B.echo()
# prints the concatenated list
X = list_concat_copy(A, B)
print "concatenation:"
X.echo()
# demonstrates that changing A does not affect X
print "changing A:"
A = B
A.echo()
print "concatenation is unaffected:"
X.echo()
def init_matrix(x_range, y_range):
matrix = []
for x in range(x_range):
temp = []
for y in range(y_range):
if random.random() > 0.5:
temp.append(cell.Cell(True))
else:
temp.append(cell.Cell(False))
matrix.append(temp)
return matrix
def createWorld(self):
"""
Creates (initiates) the world using the world.dat.
"""
# Init the world with the data from world.dat file
with open(const.WORLD_FILE, 'r') as f:
for row in range(const.WORLD_SIZE):
self.world.append([])
for col in range(const.WORLD_SIZE):
c = f.read(1)
while c not in const.WORLD_CELLS:
c = f.read(1)
if c == "E":
# Create cell of type 'earth'
self.world[row].append(
cell.Cell(echoSystem=self,
coordinates=(row, col),
cellType="earth"))
if c == "C":
# Create cell of type 'city'
self.world[row].append(
cell.Cell(echoSystem=self,
coordinates=(row, col),
cellType="city"))
if c == "F":
# Create cell of type 'forest' and update the forests counter
self.world[row].append(
cell.Cell(echoSystem=self,
coordinates=(row, col),
cellType="forest"))
self.forests += 1
if c == "S":
# Create cell of type 'sea' and update the seas counter
self.world[row].append(
cell.Cell(echoSystem=self,
coordinates=(row, col),
cellType="sea"))
self.sea += 1
if c == "G":
# Create cell of type 'glaciers' and update the glaciers count
self.world[row].append(
cell.Cell(echoSystem=self,
coordinates=(row, col),
cellType="glacier"))
self.glaciers += 1
# Let every cell update its neighbors
for row in self.world:
for column in row:
column.updateNeighbors()
def _check_and_move(self, iter_range, row_range, col_range, row_add,
col_add):
for _ in iter_range:
for row in row_range:
for col in col_range:
if self._cells[row][col].is_empty() and not self._cells[
row + row_add][col + col_add].is_empty():
self._cells[row][col] = self._cells[row +
row_add][col +
col_add]
self._cells[row + row_add][col + col_add] = cell.Cell()
elif self._cells[row][col].can_combine(
self._cells[row + row_add][col + col_add]):
self._cells[row][col].increase_value()
self._cells[row + row_add][col + col_add] = cell.Cell()
def __create_cell(self):
cells = []
for i in range(self.__NUMBER_RECTS):
for j in range(self.__NUMBER_RECTS):
cells.append(
cell.Cell(i, j, self.__R_WIDTH, self.__NUMBER_RECTS))
return cells
def _create_grid(self):
"""
Instantiates a ndims array of Cell instances that hold the value of various
quantities at certain locations in the simulation space.
Parameters:
-----------
None
Returns:
--------
grid : ndarray
An ndims dimensional array of Cell instances
"""
# Initialize empty array
grid = np.empty([self.ncells] * self.ndims, dtype=object)
# Initialize each cell in the grid. This is done using the nditer iterator in
# order to loop over each element in the ndims dimensional grid. The multi_index
# flag tells the iterator to yield the index for the current array element
it = np.nditer(grid, flags=['multi_index', 'refs_ok'])
while not it.finished:
# Get location of cell center from cell index (x0,x1,x2,...,xn). This is just
# the number of half deltas in each dimension, where delta is the width of the
# cell. The number of half deltas is just 2k + 1, where k is the cell index
# along a dimension.
ind = np.array(it.multi_index)
loc = (2 * ind + 1) * (self.cellWidth / 2.)
grid[it.multi_index] = cell.Cell(loc, self.cellWidth)
# Go to the next element. Without this, it's an infinite loop
it.iternext()
return grid
def maze(maze_map1, start1, end1):
global current_maze, temp, end, start, maze_map
maze_map = maze_map1
start = start1
end = end1
current_maze = maze_runner_initialization(maze_map)
temp = []
temp.append(start[0])
temp.append(start[1])
current_maze[temp[0]][temp[1]] = cell.Cell([temp[0], temp[1]], [temp[0], temp[1]], start, end)
current_maze[temp[0]][temp[1]].set_discovered(True)
current_maze[temp[0]][temp[1]].set_g_cost(0)
current_maze = runner_surround(maze_map, current_maze, temp[0], temp[1], start, end)
fen1.resizable(width=False, height=False)
imageFixe=PhotoImage(file='grilleMap.gif')
mon_cadre.create_image(0,0,image=imageFixe, anchor=NW)
display_mur(maze_map)
mon_cadre.pack()
update()
fen1.mainloop()
#return current_maze
return None
def create_cells(self, size=CELL_INIT_SIZE):
for i in range(self.messages["cells_y"]):
self.cells.append([])
for j in range(self.messages["cells_x"]):
self.cells[i].append(cl.Cell(size=size))
self.cells[i][j].set_location(i * size + 1, j * size + 1)
self.cells[i][j].render(self.canvas)
def fill_grid(self):
for y in range(self.y_size):
x_list = []
for x in range(self.x_size):
new_cell = cell.Cell()
x_list.append(new_cell)
self.grid.append(x_list)
def getRMP(self, parameters, debug=False):
if not self.stop:
# Simulation parameters
h.load_file('stdrun.hoc')
h.load_file('negative_init.hoc')
tstop = 100
dt = 0.025
h.stdinit()
h.celsius = 37.0
h.tstop = tstop
h.v_init = -65
# Instantiate and parameterize cells
testCell = cell.Cell(0, (0, 0), self.synvars, 'granulecell',
'output0_updated.swc')
self.parameterizeCell(testCell, parameters)
# Instrument cells
self.RMPv = h.Vector()
self.RMPv.record(testCell.c.soma[0](0.5)._ref_v)
# Run simulation
h.run()
# Get RMP
self.RMP = self.RMPv[-1]
if debug:
return [np.array([self.RMP]), np.array([self.RMPv])]
else:
return np.array([self.RMP])
else:
return 1e9
def readFile(name):
with open(name) as fd:
N,M,C,R=fd.readline().split()
N,M,C,R=int(N),int(M),int(C),int(R)
customers=[]
map=[]
for i in range(C):
col, row, reward=fd.readline().split()
row, col, reward = int(row),int(col),int(reward)
customers.append(customer.Customer(row,col,reward))
for i in range(M):
l=list(fd.readline())
map_list=[]
for j in range(N):
c=cell.Cell(l[j])
map_list.append(c)
map.append(map_list)
param = {}
param['N'] = N
param['M'] = M
param['C'] = C
param['R'] = R
return customers,map, param
def __init__(self, size, mineCount):
self.__board = dict()
self.__width = size
self.__height = size
self.__mineCount = mineCount
for x in range(0, self.__width):
for y in range(0, self.__height):
self.__board.update({ (x, y) : cell.Cell() })
# populate board with mines
while mineCount > 0:
x = random.randrange(self.__width)
y = random.randrange(self.__height)
self.__board[(x, y)].setMine()
if (self.__board[(x, y)].isMined()):
mineCount -= 1
# calculate mine counts
for x in range(0, self.__width):
for y in range(0, self.__height):
if not self.__board[(x, y)].isMined():
self.__board[(x, y)].setCount(self.__getAdjMineCount(x, y))
else:
self.__board[(x, y)].setCount(-1)
def make_game_board():
game_board = board.Board(BOARD_WIDTH, BOARD_HEIGHT)
for x in range(BOARD_WIDTH):
for y in range(BOARD_HEIGHT):
game_board._board[x][y] = cell.Cell(x, y, random.choice(states))
return game_board
def create_body(size_1, size_2):
reply = []
for x in range(size_1):
temp = []
for y in range(size_2):
temp.append(cell.Cell())
reply.append(temp)
return reply
def test_correct_click_inside(self):
input_x = 1
input_y = 1
x1 = y1 = cell_id = x = y = 0
x2 = y2 = 2
c = cell.Cell(x1, y1, x2, y2, cell_id, x, y)
expected_output = True
self.assertEqual(expected_output, c.is_click_inside(input_x, input_y))
def init_grid(self, walls):
for x in range(self.grid_width):
for y in range(self.grid_height):
if (x, y) in walls:
reachable = False
else:
reachable = True
self.cells.append(cell.Cell(x, y, reachable))
def test_correct_cell_status_change(self):
input_empty_cell = CellStatus.Empty
input_cross_cell = CellStatus.Cross
input_circle_cell = CellStatus.Circle
c = cell.Cell(0, 0, 0, 0, 0, 0, 0)
self.assertEqual(c.change_cell_type(input_empty_cell), c.status)
self.assertEqual(c.change_cell_type(input_circle_cell), c.status)
self.assertEqual(c.change_cell_type(input_cross_cell), c.status)
def loadBoard(filename):
with open(filename) as f:
content = f.readlines()
rows = len(content)
cols = len(content[0].strip().split(","))
board = [[None for x in range(rows)] for y in range(cols)]
for r in range(rows):
curRow = content[r].strip().split(",")
for c in range(cols):
curCellInt = int(curRow[c])
if curCellInt == 0:
board[r][c] = cell.Cell(False)
else:
board[r][c] = cell.Cell(True)
return board
def upcast_logic_cell(logic_cell, root, width, height):
this_cell = cell.Cell(root,
color=logic_cell.color,
width=width,
height=height,
row=logic_cell.row,
column=logic_cell.column)
return this_cell
def getMembraneTimeConstant(self, parameters, debug=False):
if not self.stop:
######################################
# Membrane Time Constant Experiments #
######################################
# Simulation parameters
h.load_file('stdrun.hoc')
h.load_file('negative_init.hoc')
tstop = self.subthresh_dur + 300
dt = 0.025
h.stdinit()
h.celsius = 37.0
h.tstop = tstop
h.v_init = -65
# Instantiate and parameterize cells
testCell = cell.Cell(0, (0, 0), self.synvars, 'granulecell',
'output0_updated.swc')
self.parameterizeCell(testCell, parameters)
# Make sure the cell doesn't spike
# Create inputs for experiments
stim = h.IClamp(0.5, sec=testCell.c.soma[0])
stim.amp = self.threshAmp # amp at which neuron no longer spikes
stim.dur = self.subthresh_dur # subthresh is duration where neuron no longer spikes
stim.delay = 0
# Instrument cells
self.tauV = h.Vector()
self.tauV.record(testCell.c.soma[0](0.5)._ref_v)
t = h.Vector()
t.record(h._ref_t)
tvec = h.Vector()
nc = testCell.connect_pre(None, 0, 0)
nc.record(tvec)
# Run simulation
h.run()
# Calculate membrane time constant
self.tauV = np.array(self.tauV)
t = np.array(t)
t_idx = t >= self.subthresh_dur
t = t[t_idx] - self.subthresh_dur
v = self.tauV[t_idx]
try:
popt, pcov = curve_fit(self.expFunc, t, v, p0=(1, -0.1, -60))
self.tau = -1 / popt[1]
except RuntimeError:
self.tau = 1000
if debug:
return [np.array([self.tau]), v, t, popt]
else:
return np.array([self.tau])
else:
return 1e9
def test_one_operation(self):
'''Test how long one operation takes. Subtract baseline of cell creation (empty sequence)...'''
sequences = [
('Baseline', ';XXXXXXXXXXXXXXXXXXXXXX;'), #baseline: cell and unit creation, one round. no action
('Protection', ';Q1[]TT1SXXXXXXXXTTXXXX;'), #one protection
('Promoter', ';N1[]1SP1N1[]1XXXXXXXXX;'), #one promoter
('Restriction', ';R1[]T!T1SXXXXXXXXXTTXX;'), #one cut
('Ligation', ';L1[]T!T1SXXXXXT;;TXXXX;'), #one ligation
('Mutation', ';M1[]1SXXXXXXXXXXXXXXXX;'), #one mutation
('Copy', ';O1[]T!T1SXXXXXXXTTXXXX;'), #one copy
('Degradation', ';D1[]TT1XXXXXXXXXTTXXXX;'), #one degradation
('Factor', ';N1[]1F1[]T!T1SPTTXXXXX;'), #one transcription factor
('Export', ';E1[]T!T1SXXXTTXXXXXXXX;'), #one export
('Four Units', ';N0[]1N0[]1N0[]1N0[]1XX;'), #a unit exporting itself into the pool
('Unit Export', ';U1(self)[](self)2XXXXX;'),
('Substance Creation', ';V1[]()(a)1XXXXXXXXXXXX;'),
('Multi Creation', ';V1[]()(a,b,c,d,e,f,g)1;'),
('3x Promoter', ';N3[]1SP3N1[]1XXXXXXXXX;')
]
num_cells = 2500
print '\nTime per operation of a specific unit (average over {0} cells):\n'.format(num_cells)
res_dict = {}
for label, seq in sequences:
before = time.time()
for i in range(num_cells):
c = cell.Cell(seq)
c.read_seq()
c.run_all()
res_dict[label] = ((time.time() - before), seq)
baseline = res_dict['Baseline'][0]
for test in res_dict.keys():
per_cell = 1000 * (res_dict[test][0] - baseline) / num_cells
res_dict[test] = ( per_cell , res_dict[test][1] )
res = {}
for k in res_dict.keys():
res[k] = res_dict[k][0]
sorted_res = sorted(res.iteritems(), key=operator.itemgetter(1))
print 'Baseline (subtracted from all other): {1} ms / cell\nSequence: {0}'.format(res_dict['Baseline'][1], baseline)
print 'All tests ordered by time / action:\n'
for i in range(1, len(sorted_res)):
current = sorted_res[i]
percentage = round(current[1]/(baseline / 100),1)
position = '{0}. {1}: {2}\n'.format(i, current[0], res_dict[current[0]][1])
position += '\t{0}% of baseline time, {1} ms / action'.format(percentage, round(current[1], 4))
print position
#wait, so that end message of test does not conflict with printing of last results
time.sleep(0.1)
def load(self, filename):
self.blank_board()
with open(filename, 'r') as maz_file:
for line in maz_file:
line = line.strip("\n")
my_cell = cell.Cell()
row, col = my_cell.deserialize(line)
self.board[row][col] = my_cell
def __init__(self):
self.board = []
self.board_length = 9
self.allDiffsLen = 3
self.checkAll = ((0, 0), (1, 3), (2, 6), (3, 1), (4, 4), (5, 7),
(6, 2), (7, 5), (8, 8))
for y in range(self.board_length):
row = [cell.Cell() for x in range(self.board_length)]
self.board.append(row)
def ini_cell(self, size):
cells = []
cells_line = []
for i in range(size):
for j in range(size):
cells_line.append(cell.Cell(i, j))
cells.append(cells_line)
cells_line = []
return cells
def __init__(self, filepart, x):
self.cells = []
print("@%i - %s" % (x, filepart))
self.x = x
y = 0
for l in filepart.split("|"):
self.cells.append(cell.Cell(l, x, y))
y += 1
print("%i cells in this line" % len(self.cells))
def __init__(self, height=4, width=4):
self._height = height
self._width = width
self._cells = []
for _ in range(self.height):
new_row = []
for _ in range(self.width):
new_row.append(cell.Cell(0))
self._cells.append(new_row)