def compute_trajectory_prediction_mse(args, ground_truth, predictions):
"""
inputs:
args: model parameters
ground_truth: list of groudn truth velocities in absolute frame
predictions: list of predicted velocities """
avg_mse = 0
cnt = 0
mse_list = []
for pred, gt in zip(predictions, ground_truth):
avg_mse = 0
cnt = 0
# compute average per trajectory
# tbp_len
# path from vel for vel
for t in range(len(pred)):
# real trajectory global frame
real_vel_global_frame = gt.vel_vec[t + args.prev_horizon + 1:t +
args.prediction_horizon +
args.prev_horizon + 1, :2]
real_traj_global_frame = sup.path_from_vel(
initial_pos=np.array([0, 0]),
pred_vel=real_vel_global_frame,
dt=args.dt)
# pred_horizon = 10
vel_pred = np.zeros((args.prediction_horizon, args.output_dim))
error = 0
# [1,144]
pred_t = pred[t][0]
min_error = np.zeros((pred_t.shape[0]))
# 144 -> prediction_horizon*output_state_dim = 4*n_mixture
for sample_id in range(pred_t.shape[0]):
error = np.zeros((args.n_mixtures))
for mix_idx in range(args.n_mixtures):
# plot predicted trajectory global frame
for i in range(args.prediction_horizon):
idx = i * args.output_pred_state_dim * args.n_mixtures + mix_idx
idy = i * args.output_pred_state_dim * args.n_mixtures + mix_idx + args.n_mixtures
if args.normalize_data:
mu_x = pred_t[sample_id,
idx] / args.sx_vel + args.min_vel_x
mu_y = pred_t[sample_id,
idy] / args.sy_vel + args.min_vel_y
else:
mu_x = pred_t[sample_id, idx]
mu_y = pred_t[sample_id, idy]
vel_pred[i, :] = [mu_x, mu_y]
traj_pred = sup.path_from_vel(initial_pos=np.array([0, 0]),
pred_vel=vel_pred,
dt=args.dt)
for pred_step in range(args.prediction_horizon):
error[mix_idx] += np.linalg.norm(
real_traj_global_frame[pred_step, :] -
traj_pred[pred_step, :]) / args.prediction_horizon
min_error[sample_id] = min(error)
avg_mse = (avg_mse * cnt + min(min_error)) / (cnt + 1)
cnt += 1
mse_list.append(avg_mse)
return avg_mse, mse_list
def plot(self, ax, x_scale=1, y_scale=1):
"""
Plots the trajectories and the static occupancy grid of all agents in this container.
"""
colormap = pl.get_cmap('rainbow')
c_norm = pl.matplotlib.colors.Normalize(vmin=0,
vmax=len(
self.agent_data.keys()))
scalar_color_map = pl.cm.ScalarMappable(norm=c_norm, cmap=colormap)
for cnt, id in enumerate(self.agent_data.keys()):
color_value = scalar_color_map.to_rgba(cnt)
self.agent_data[id].plot(ax,
color=color_value,
x_scale=1,
y_scale=1)
#sup.plot_grid(ax, np.array([self.occupancy_grid.center[0], self.occupancy_grid.center[1]]), self.occupancy_grid.gridmap, self.occupancy_grid.resolution, self.occupancy_grid.map_size)
sup.plot_grid(ax, np.array([0, 0]), self.occupancy_grid.gridmap,
self.occupancy_grid.resolution,
self.occupancy_grid.map_size)
ax.set_xlim(
[-self.occupancy_grid.center[0], self.occupancy_grid.center[0]])
ax.set_ylim(
[-self.occupancy_grid.center[1], self.occupancy_grid.center[1]])
ax.set_aspect('equal')
def delete(self, start, size, allele):
if allele.lower() == "m":
if start > self.maternalHaplotypeLength:
raise ValueError(
"The starting point of a mutation cannot be over maternal-haplotype-chromosome length!"
)
else:
startbin, endbin = Support.startendbins(
bins=self.maternalHaplotype, start=start, size=size)
self.maternalHaplotype = self.maternalHaplotype[
0:startbin] + self.maternalHaplotype[endbin:]
self.maternalHaplotypeLength = sum(
seg[1] - seg[0] for seg in self.maternalHaplotype)
elif allele.lower() == "p":
if start > self.paternalHaplotypeLength:
raise ValueError(
"The starting point of a mutation cannot be over paternal-haplotype-chromosome length!"
)
else:
startbin, endbin = Support.startendbins(
bins=self.paternalHaplotype, start=start, size=size)
self.paternalHaplotype = self.paternalHaplotype[
0:startbin] + self.paternalHaplotype[endbin:]
self.paternalHaplotypeLength = sum(
seg[1] - seg[0] for seg in self.paternalHaplotype)
else:
raise ValueError(
"The specified allele should be equal to either M or P (non-case sensitive)!"
)
def parse_data(path, verbose=1):
first = True
second = True
k = 0
counter = 0
with open(path, "r") as inputFile:
for line in inputFile:
if first:
first = False
tokens = line.split(",")
input_size = int(tokens[0])
output_size = int(tokens[1])
samples_size = int(tokens[2])
inputs = numpy.zeros((samples_size, input_size))
outputs = numpy.zeros((samples_size, output_size))
elif second:
second = False
if verbose:
Support.colored_print("Parameters: ", "blue")
Support.colored_print(line, "blue")
else:
counter += 1
if counter < samples_size:
input, output = line.split('=')
for i, e in enumerate(input.split()):
inputs[k][i] = float(e.strip())
for i, e in enumerate(output.split()):
outputs[k][i] = float(e.strip())
k += 1
else:
break
return inputs, outputs, input_size, output_size
def generateControl(self, gameData, playerId):
act = Support.randomFromList(self.actionName)
fr = Support.randomFromList(self.firstName)
sc = Support.randomFromList(self.secondName)
th = Support.randomFromList(self.thirdName)
fullName = act + " " + fr + " " + sc + " " + th
print "Generated control with name " + fullName
return Control(playerId, fullName, str(gameData.getFreeControlId()))
def pipeline(img, isVideo=False):
# Image Preprocessing
undst, binary, binary_warped = PreProcessing.preprocess_image(img)
# Lane Detection Code Start
lanes, leftx, lefty, rightx, righty, ploty = LaneFinding.get_lane_lines(
binary_warped, isVideo)
lcurve, rcurve = Support.get_real_lanes_curvature(ploty, leftx, lefty,
rightx, righty)
output = draw_lane_area(undst, binary_warped, ploty, leftx, lefty, rightx,
righty, isVideo)
left_fit, right_fit, dummy = Support.fit_polylines(binary_warped.shape[0],
leftx,
lefty,
rightx,
righty,
x_scale_factor=1,
y_scale_factor=1)
left_fitx, right_fitx = Support.get_polylines_points(
ploty, left_fit, right_fit)
if (isVideo is True):
lcurve, rcurve = getSmoothedCurveData(lcurve, rcurve)
left_fitx, right_fitx = getSmoothedLanesData(left_fitx, right_fitx)
shiftFromLaneCenter_m, side = calculate_shift_from_lane_center(
binary_warped, left_fitx, right_fitx)
Font = cv2.FONT_HERSHEY_SIMPLEX
color = (255, 255, 255)
cv2.putText(output, 'curve = ' + str((lcurve + rcurve) / 2) + ' m',
(10, 100), Font, 1, color, 2, cv2.LINE_AA)
cv2.putText(
output, 'Vehicle is ' + str(shiftFromLaneCenter_m) + ' (m) ' + side +
' of lane center', (10, 150), Font, 1, color, 2, cv2.LINE_AA)
# Lane Detection Code End
# Vehicle Detection Code Start
cars_boxs = get_classified_cars_boxs(undst)
classified_boxs = Visualisation.draw_boxes(undst,
cars_boxs,
color=(0, 0, 255),
thick=6)
filtered_boxs, heat_map = get_heat_map_boxs(cars_boxs, undst, isVideo)
output = Visualisation.draw_boxes(output,
filtered_boxs,
color=(0, 0, 255),
thick=6)
# Vehicle Detection Code End
return undst, classified_boxs, heat_map, output
async def search(message, args):
"""
Sending a git hub search result
https://github.com/nosv1/jc/search?q=&type=wikis
"""
jc = Support.get_jc_from_channel(message.channel)
query = " ".join(args[2:]).strip()
results = None
if query:
results = Support.search_github(query)
results_description = ""
outputted = 0
for result in results:
if len(results_description) < 1000:
outputted += 1
# **title** - `command`
title = result['title'].split("`") # title should be >> title `command` >> [title, command, '']
command = title[1] if len(title) > 1 else ""
results_description += f"**{title[0]}** - `{command}`\n"
# results_description += f"**[{title[0]}]({result['link']})**" + (f" - `{command}`\n" if command else "\n")
# p = result['p'].split("\n") + [" "] # [@jc command help, snippet]
# results_description += f"`{p[0].strip().replace('**', '')}`\n\n"
# \/ old, used to be Title \n Command \n Body
# results_description += f"`{p[0].strip().replace('**', '')}`\n{p[1].strip()}\n\n"
if not results_description: # no results
results_description += f"{jc} help\n"
await Support.simple_bot_response(message.channel,
title = f"{len(results)} Result{'s' if outputted != 1 else ''}",
description=results_description
)
Logger.log("search", results_description)
else:
description = f"`@{jc} ? <search_words>`\n"
description += f"`@{jc} ? custom embeds`"
await Support.simple_bot_response(message.channel,
title="No Search Words Provided",
description=description,
reply_message=message
)
Logger.log("Bot Reponse", "Simple Help Search")
def plot(self):
#画两端结点
x=[self.a1,self.a2]
y=[self.b1,self.b2]
plt.scatter(x,y,c='w',marker='o', s=60,edgecolors=self.pc,linewidths=self.c1*self.l, zorder=100)#s是点大小
#画杆
plt.plot(x,y,c=self.tc,linewidth=self.c2*self.l,zorder=1)
#画支座
sp1=Support.Support(self.sx1,self.sy1,self.a1,self.b1,self.l,self.sc)
sp1.display()
sp2=Support.Support(self.sx2,self.sy2,self.a2,self.b2,self.l,self.sc)
sp2.display()
plt.tight_layout()
def logArgs(args):
Support.log('\n'.join(["Arguments:"] + [
'\t{}:\t{}'.format(arg, args[arg])
for arg in args if arg != 'mutations'
] + [""]),
level="INFO")
Support.log('\n'.join(["Mutations:"] + [
'\t{}:\t{}'.format(mut, args['mutations'][mut])
for mut in args['mutations']
if mut != 'clonalfocal' and mut != 'subclonalfocal'
] + [""]),
level="INFO")
if 'clonalfocal' in args['mutations']:
Support.log('\n'.join(['Clonal focal CNAs:'] + [
'\tmean_len= {}, standard_deviation= {}, quantity= {}'.format(
key[0], key[1], args['mutations']['clonalfocal'][key])
for key in args['mutations']['clonalfocal']
] + [""]),
level="INFO")
if 'subclonalfocal' in args['mutations']:
Support.log('\n'.join(['Subclonal focal CNAs:'] + [
'\tmean_len= {}, standard_deviation= {}, quantity= {}'.format(
key[0], key[1], args['mutations']['subclonalfocal'][key])
for key in args['mutations']['subclonalfocal']
] + [""]),
level="INFO")
def draw_hangman(lives):
if lives == 5:
sup.draw("Lives 5.txt")
if lives == 4:
sup.draw("Lives 4.txt")
if lives == 3:
sup.draw("Lives 3.txt")
if lives == 2:
sup.draw("Lives 2.txt")
if lives == 1:
sup.draw("Lives 1.txt")
def DisplaySupportType():
"""
Purpose: List all Support type for products.
Argument(s): None
Return: list of Suppport types.
"""
#SUPPORT MODULE FOR THE SUPPORT CLASS ( TABLE )
#----------------------------------------------
import Support
#SUPPORT OBJECT
#--------------
NewSupport = Support.Support()
Supports = NewSupport.getAllSupport()
count = 1
if (len(Supports) != 0):
print "No. REFERENCE NO. START DATE END DATE SUPPORT LEVEL"
print "--- ------------- ---------- -------- -------------"
for support in Supports:
print "{0} {1:15} {2:15} {3:15} {4}".format(
count, support[1], support[2], support[3], support[4])
count = count + 1
def gradients(self, x, loss_function, y_target):
'''
Inputs:
x: network input
loss_function: Since the gradients of the loss function need to be computed, this has to be provided.
y_target: Target values for the network output.
Return value:
gradients: Gradients of the loss function w.r.t. all weights and biases of the network.
Gradients have a weights and biases member, the indexing starts with 0 for the first hidden layer (W_1, b_1)
and ends with the output layer (W_out, b_out)
'''
gradients = sup.Variables()
# Outputs of each layer (layer_evaluations[0] is input x)
layer_evaluations = []
for layer_idx, layer in enumerate(self.layers):
layer_evaluations.append(self.evaluateLayer(layer_idx, x))
# Output equals the evaluation of the last layer
network_output = self.output(x)
# Derivative of cost w.r.t. the network output
dCost_dy = #TODO: implement cost function derivative w.r.t. output variables of network
# Element-wise multiplication with sigmoid derivative (sigmoid is applied element-wise)
delta_fused = #TODO: start backpropagating the error
# Gradient backpropagation
## Start from last layer and propagate error gradient through until first layer
## Attention!!!: layer_evaluations[0] is the network input while self.layers[0] is the first hidden layer
for layer_idx in np.arange(len(self.layers)-1, -1, -1):
logger.debug('Computing the gradient for layer {}'.format(layer_idx))
# If layer is not last layer, update delta_fused (which is accumulating the back-propagated gradient)
# TODO: implement backpropagation of gradient for arbitrary number of layers
return gradients
def runL1000CDS2(infile, outfile):
# Read infile
cdDataframe = pd.read_table(infile, index_col='gene_symbol').fillna(0)
# Initialize dataframes
linkDataframe = pd.DataFrame()
signatureDataframe = pd.DataFrame()
# Loop through timepoints
for comparison in cdDataframe.columns:
# Run L1000CDS2
resultDict = S.getL1000CDS2Results(cdDataframe, comparison)
# Add comparison labels
resultDict['links']['comparison'] = comparison
resultDict['signatures']['comparison'] = comparison
# Append dataframes
linkDataframe = pd.concat([linkDataframe, resultDict['links']])
signatureDataframe = pd.concat(
[signatureDataframe, resultDict['signatures']])
# Write files
linkDataframe.to_csv(outfile, sep='\t', index=False)
signatureDataframe.to_csv(outfile.replace('links', 'signatures'),
sep='\t',
index=False)
def build_new(self):
logger.info("Build New")
self.allunits = []
self.factions = {}
self.allreinforcements = {}
self.prefabs = []
self.objective = None
self.phase_music = None
self.map = None
self.game_constants = Counter()
self.game_constants['level'] = 0
self.game_constants['money'] = 0
self.convoy = []
self.play_time = 0
self.support = Support.Support_Graph(
'Data/support_nodes.txt',
'Data/support_edges.txt') if cf.CONSTANTS['support'] else None
self.unlocked_lore = []
self.statistics = []
self.market_items = set()
self.sweep()
self.generic()
# Turn tutorial mode off if the difficulty does not start with a tutorial
if not int(self.mode['tutorial']):
cf.OPTIONS['Display Hints'] = 0
def plot(self):
#画两端结点
x = [self.a1, self.a2]
y = [self.b1, self.b2]
plt.scatter(x,
y,
c='w',
marker='o',
s=self.c8 * self.l,
edgecolors=self.pc,
linewidths=self.c7 * self.l,
zorder=100) #s是点大小
#画杆
plt.plot(x, y, c=self.tc, linewidth=self.c6 * self.l, zorder=1)
#画支座
sp1 = Support.Support(self.sx1, self.sy1, self.a1, self.b1, self.l,
self.sc)
sp1.display()
sp2 = Support.Support(self.sx2, self.sy2, self.a2, self.b2, self.l,
self.sc)
sp2.display()
#画力
pass
#标数据
l1 = np.array([self.a1, self.b1])
l2 = np.array([self.a2, self.b2])
#计算角度
if self.a1 == self.a2:
if self.b1 > self.b2:
angle = -90
else:
angle = 90
else:
angle = math.atan((self.b2 - self.b1) /
(self.a2 - self.a1)) / (2 * math.pi) * 360
plt.text((l1[0] + l2[0]) / 2, (l1[1] + l2[1]) / 2,
str(self.result),
fontsize=self.c5 * self.l,
rotation=angle,
rotation_mode='anchor',
zorder=1000)
#画外力
f1 = Force.Force(self.a1, self.b1, self.fx1, self.fy1, self.l, self.ax)
f1.ForcePlot()
f2 = Force.Force(self.a2, self.b2, self.fx2, self.fy2, self.l, self.ax)
f2.ForcePlot()
def getSendDataHandler(participant,topic): localInterface = Support.doSubnetTranslation(topic.localInterface) if topic.transport == TRANSPORT_MC: return McSendDataHandler(localInterface,topic,topic.timeToLive) if topic.transport == TRANSPORT_UDP: return UdpSendDataHandler(topic) return None
def __init__(self, name, length, binsize):
self.name = name
self.length = length
self.binsize = binsize
self.reference = Support.bins(size=self.length, step=self.binsize)
self.maternalHaplotype = copy.deepcopy(self.reference)
self.maternalHaplotypeLength = copy.deepcopy(self.length)
self.paternalHaplotype = copy.deepcopy(self.reference)
self.paternalHaplotypeLength = copy.deepcopy(self.length)
def draw_lane_area(undist,
warped,
ploty,
leftx,
lefty,
rightx,
righty,
isVideo=False):
left_fit, right_fit, dummy = Support.fit_polylines(warped.shape[0],
leftx,
lefty,
rightx,
righty,
x_scale_factor=1,
y_scale_factor=1)
left_fitx, right_fitx = Support.get_polylines_points(
ploty, left_fit, right_fit)
if (isVideo is True):
left_fitx, right_fitx = getSmoothedLanesData(left_fitx, right_fitx)
# Create an image to draw the lines on
warp_zero = np.zeros_like(warped).astype(np.uint8)
color_warp = np.dstack((warp_zero, warp_zero, warp_zero))
# Recast the x and y points into usable format for cv2.fillPoly()
pts_left = np.array([np.transpose(np.vstack([left_fitx, ploty]))])
pts_right = np.array(
[np.flipud(np.transpose(np.vstack([right_fitx, ploty])))])
pts = np.hstack((pts_left, pts_right))
# Draw the lane onto the warped blank image
cv2.fillPoly(color_warp, np.int_([pts]), (0, 255, 0))
# Warp the blank back to original image space using inverse perspective matrix (Minv)
newwarp = cv2.warpPerspective(color_warp, Minv,
(undist.shape[1], undist.shape[0]))
# Combine the result with the original image
result = cv2.addWeighted(undist, 1, newwarp, 0.3, 0)
return result
def __init__(self, reference, snplist, snpratio, HEHOratio, ignorelist):
self.reference = reference
self.snplist = Support.parseSNPList(snplist)
self.snpratio = snpratio
self.HEHOratio = HEHOratio
self.ignorelist = ignorelist
self.chromosomes = []
self.lengths = {}
self.maternalfa = None
self.paternalfa = None
self.numsnps = 0
self.hetsnps = 0
def evaluate(path_network, input):
Support.colored_print("Loading neural network...", "blue")
neural_network = NeuralNetwork.NeuralNetwork()
neural_network.load(path_network)
Support.colored_print("Evaluating...", "blue")
result = neural_network.evaluate(input)
Support.colored_print(result, "pink")
def Find_Line(filtered_mask):
im2, contours, hierarchy = cv2.findContours(filtered_mask, cv2.RETR_LIST,
cv2.CHAIN_APPROX_SIMPLE)
r, c = 400, 400
dp = cv2.cvtColor(filtered_mask, cv2.COLOR_GRAY2BGR)
cv2.line(dp, (c // 2, 1), (c // 2, r), (255, 0, 0), 5)
midPoint = c // 2
maxArea = 0
offset = 0.0
angle = 0.0
for cntrs in contours:
mu = cv2.moments(cntrs, False)
x, y, w, h = cv2.boundingRect(cntrs)
#if mu['m00'] > 120.0:
if True:
cx = x + (w // 2) # centre point
area = mu['m00']
if area > maxArea:
maxArea = area
offset = midPoint - cx
#offset = cx
angle = math.atan2(w if offset >= 0 else -w, h)
cv2.rectangle(dp, (x, y), (x + w, y + h), (0, 255, 0), 2)
else:
cv2.rectangle(dp, (x, y), (x + w, y + h), (0, 0, 255), 2)
#print(area, cx, maxArea)
cv2.imshow("frame", dp)
angle = int(Support.remap(angle, -math.pi / 2, math.pi / 2, 0, 255))
offset = int(127 - Support.remap(offset, 0, c, 0, 255))
return offset, angle
def is_lane_curvature_accepted(ploty, leftx, lefty, rightx, righty):
left_curverad, right_curverad = Support.get_real_lanes_curvature(
ploty, leftx, lefty, rightx, righty)
print(left_curverad, right_curverad)
if left_curverad > 2000 and right_curverad > 2000:
return True # Almost straight lanes
elif (left_curverad < 80 or right_curverad < 80):
return False
# elif (left_fit[0] > 0 and right_fit[0] < 0) or (right_fit[0] > 0 and left_fit[0] < 0):
# return False # same curvature wit opposite direction
else:
return True
async def set_invite_link(message, args, author_perms):
"""
"""
jc = Support.get_jc_from_channel(message.channel)
guild = message.guild if message.guild else message.author
jc_guild = get_jc_guild(guild.id)
if not jc_guild: # if not in db, create new one
jc_guild = Guild(
guild.id,
prefix=f"@{Support.get_jc_from_channel(message.channel)}")
jc_guild.name = guild.name # set some attrs
jc_guild.guild = guild if message.guild else None
jc_guild.edit_guild()
if validators.url(args[2]): # link provided
if message.guild and not author_perms.create_instant_invite: # missing permission
await Support.missing_permission("Create Invite", message)
return
jc_guild.invite_link = args[2]
await simple_bot_response(
message.channel,
description=
f"**{jc_guild.name}'s Default Event Invite Link:** {jc_guild.invite_link}"
)
elif args[2]: # invalid link
await simple_bot_response(
message.channel,
title="Invalid Link",
description=f"`@{jc} {args[1]} <invite_link>`",
reply_message=message)
else: # no link provided
description = f"**{jc_guild.name}'s Default Event Invite Link:** {jc_guild.invite_link if jc_guild.invite_link else '`None Provided`'}\n\n"
description += f"`@{jc} {args[1]} <invite_link>`"
await simple_bot_response(message.channel,
description=description,
reply_message=message)
jc_guild.edit_guild()
def basesize(isize):
size = 0
try:
if isize[-2:] == "kb":
size = int(isize[:-2]) * 1000
elif isize[-2:] == "Mb":
size = int(isize[:-2]) * 1000000
else:
size = int(isize)
return size
except:
raise ValueError(
sp.error(
"Size must be a number, optionally ending with either \"kb\" or \"Mb\"!"
))
def guess_character(selected_word, guessed_chars):
"Prompts the user to make a guess"
indexes = []
char = input("Try and guess a character: ")
char = char.lower()
selected_word = selected_word.lower()
if char in selected_word and not(char in guessed_chars):
print("YOu guessed correctly!")
indexes = sup.find_in_string(selected_word, char)
return indexes, [char]
elif char in guessed_chars:
print("You already guessed that dummy")
return [-2], []
else:
print("You guessed incorrectly ;(")
return [-1], [char]
def generateTasks (self , gameData, fixedTask=None, fixedTime=None):
for (pid, pdata) in gameData.player.iteritems():
if not gameData.hasTasks (pid):
print "Generating task for player " + pid
acts = gameData.getPossibleActions()
if len(acts) > 0:
if fixedTask == None:
ourAct = Support.randomFromList(acts)
else:
ourAct = acts[fixedTask]
if fixedTime == None:
runtime = random.randint(self.taskTime[0], self.taskTime[1])
else:
runtime = fixedTime
gameData.currentTasks += [ Task(ourAct[1], ourAct[0], pid, runtime) ]
print "> Task added"
def testBatchGradient(self):
# Manually build a gradient list
gradient_list = []
n_layers = 2
batch_size = 3
w = np.ones([3, 5])
b = np.ones([1, 5])
grad = sup.Variables()
for i in range(n_layers):
grad.weights.append(w)
grad.biases.append(b)
for j in range(batch_size):
gradient_list.append(grad)
# Manually compute batch gradient
batch_gradient_manual = grad * batch_size
batch_gradient = self.optimizer.computeBatchGradient(gradient_list)
self.assertTrue(batch_gradient_manual == batch_gradient)
def testVariables(self):
var = sup.Variables()
var.weights.append(np.ones([2, 2]))
var.weights.append(np.ones([2, 2]))
var.biases.append(np.ones([1, 2]))
var.biases.append(np.ones([1, 2]))
# Multiplication
var_neg = var * (-1)
for i in range(len(var)):
self.assertTrue(
np.all(var.weights[i] +
var_neg.weights[i] == np.zeros_like(var.weights[i])))
self.assertTrue(
np.all(var.biases[i] +
var_neg.biases[i] == np.zeros_like(var.biases[i])))
# Addition
var_add = var + var_neg
for i in range(len(var_add)):
self.assertTrue(
np.all(var_add.weights[i] == np.zeros_like(var.weights[i])))
self.assertTrue(
np.all(var_add.biases[i] == np.zeros_like(var.biases[i])))
# Subtraction
var_sub = var - var
for i in range(len(var_sub)):
self.assertTrue(
np.all(var_sub.weights[i] == np.zeros_like(var.weights[i])))
self.assertTrue(
np.all(var_sub.biases[i] == np.zeros_like(var.biases[i])))
# Equality
self.assertTrue(var == var)
self.assertFalse(var == var_sub)
# Inequality
self.assertFalse(var != var)
self.assertTrue(var != var_sub)
def submitEnrichrGenesets(infile, outfile):
# Read infile
cdDataframe = pd.read_table(infile, index_col='gene_symbol').fillna(0)
# Initialize link dataframe
resultDataframe = pd.DataFrame()
# Loop through timepoints
for comparison in cdDataframe.columns:
# Get Enrichr links
enrichrLinkDataframe = S.uploadToEnrichr(cdDataframe, comparison)
# Add comparison label
enrichrLinkDataframe['comparison'] = comparison
# Concatenate
resultDataframe = pd.concat([resultDataframe, enrichrLinkDataframe])
# Save data
resultDataframe.to_csv(outfile, sep='\t', index=False)
def getReceiveDataHandler(participant,topic): key = __makeKey(topic) rdh = None if key in __ReceiveDataHandler: rdh = __ReceiveDataHandler[key] if max(rdh.topic.sampleMaxSize,topic.sampleMaxSize) > PACKET_MAX_SIZE: message = "Warning: " if topic.transport == TRANSPORT_UDP: message += "UDP Transport" else: message += "Same port (%s)" % topic.port message += " is used with Topics with 'sampleMaxSize' > %s" % PACKET_MAX_SIZE print message else: localInterface = Support.doSubnetTranslation(topic.localInterface) if topic.transport == TRANSPORT_MC: rdh = McReceiveDataHandler(localInterface,topic) if topic.transport == TRANSPORT_UDP: rdh = UdpReceiveDataHandler(localInterface,topic) rdh.start() __ReceiveDataHandler[key] = rdh return rdh
def build_new(self):
logger.info("Build New")
self.allunits = []
self.groups = {}
self.allreinforcements = {}
self.prefabs = []
self.objective = None
self.map = None
self.counters = {}
self.counters['level'] = 0
self.convoy = []
self.counters['money'] = 0
self.play_time = 0
self.game_constants = []
self.support = Support.Support_Graph(
'Data/support_nodes.txt',
'Data/support_edges.txt') if cf.CONSTANTS['support'] else None
self.modify_stats = cf.read_growths_file()
self.unlocked_lore = []
self.statistics = []
self.market_items = set()
self.sweep()
self.generic()
def getEnrichrResults(infile, outfile):
# Read infile
enrichrLinkDataframe = pd.read_table(infile,
index_col=['geneset', 'comparison'])
# Initialize result dataframe
resultDataframe = pd.DataFrame()
# Set libraries
libraries = [
'ChEA_2016', 'KEGG_2016', 'GO_Biological_Process_2015',
'GO_Cellular_Component_2015', 'GO_Molecular_Function_2015', 'VirusMINT'
]
# Loop through timepoints, genesets and libraries
for geneset in enrichrLinkDataframe.index.levels[0]:
for comparison in enrichrLinkDataframe.index.levels[1]:
for library in libraries:
# Get enrichment results
enrichmentResultDataframe = S.getEnrichmentResults(
enrichrLinkDataframe.loc[(geneset, comparison),
'userListId'], library)
# Add labels
enrichmentResultDataframe['comparison'] = comparison
enrichmentResultDataframe['geneset'] = geneset
enrichmentResultDataframe['library'] = library
# Concatenate
resultDataframe = pd.concat(
[resultDataframe, enrichmentResultDataframe])
# Write file
resultDataframe.to_csv(outfile, sep='\t', index=False)
def load(self, load_info):
logger.info("Load")
# Rebuild gameStateObj
self.allunits = [
UnitObject.UnitObject(info) for info in load_info['allunits']
]
self.factions = load_info['factions'] if 'factions' in load_info else (
load_info['groups'] if 'groups' in load_info else {})
self.allreinforcements = load_info['allreinforcements']
self.prefabs = load_info['prefabs']
self.triggers = load_info.get('triggers', dict())
map_info = load_info['map']
self.playtime = load_info['playtime']
self.convoy = [
ItemMethods.deserialize(item_dict)
for item_dict in load_info['convoy']
]
self.convoy = [item for item in self.convoy if item]
self.turncount = load_info['turncount']
self.game_constants = load_info['game_constants']
self.level_constants = load_info['level_constants']
self.objective = CustomObjects.Objective.deserialize(
load_info['objective']) if load_info['objective'] else None
self.phase_music = CustomObjects.PhaseMusic.deserialize(
load_info['phase_music']) if load_info['phase_music'] else None
support_dict = load_info['support']
self.talk_options = load_info['talk_options']
self.base_conversations = load_info['base_conversations']
self.stateMachine = StateMachine.StateMachine(
load_info['state_list'][0], load_info['state_list'][1])
self.statistics = load_info['statistics']
# self.message = [Dialogue.Dialogue_Scene(scene) for scene in load_info['message']]
self.message = []
self.unlocked_lore = load_info['unlocked_lore']
self.market_items = load_info.get('market_items', set())
self.mode = load_info.get('mode', self.default_mode())
# Map
self.map = SaveLoad.create_map('Data/Level' +
str(self.game_constants['level']))
if map_info:
self.map.replay_commands(map_info['command_list'],
self.game_constants['level'])
self.map.command_list = map_info['command_list']
for position, current_hp in map_info['HP']:
self.map.tiles[position].set_hp(current_hp)
# Statuses
for index, info in enumerate(load_info['allunits']):
for s_dict in info['status_effects']:
if isinstance(s_dict, dict):
StatusObject.deserialize(s_dict, self.allunits[index],
self)
else:
self.allunits[index].status_effects.append(s_dict)
# Support
if cf.CONSTANTS['support']:
self.support = Support.Support_Graph('Data/support_nodes.txt',
'Data/support_edges.txt')
self.support.deserialize(support_dict)
else:
self.support = None
# Set up blitting surface
if self.map:
mapSurfWidth = self.map.width * GC.TILEWIDTH
mapSurfHeight = self.map.height * GC.TILEHEIGHT
self.mapSurf = Engine.create_surface((mapSurfWidth, mapSurfHeight))
self.grid_manager = AStar.Grid_Manager(self.map)
self.boundary_manager = CustomObjects.BoundaryManager(self.map)
for unit in self.allunits:
if unit.position:
self.grid_manager.set_unit_node(unit.position, unit)
self.generic()
if 'phase_info' in load_info:
self.phase.current, self.phase.previous = load_info['phase_info']
def gradient_descent(train_elements,
alpha,
numIterations,
k,
verbose=0,
jump_enabled=0):
inputs = []
outputs = []
for e in range(0, len(train_elements)):
inputs.append(train_elements[e].input)
outputs.append(train_elements[e].output)
x = numpy.asarray(inputs)
y = numpy.asarray(outputs)
m, n = numpy.shape(x)
theta = numpy.ones(n)
x_trans = x.transpose()
counter_for_jump = 0
previous_cost = 0
for i in range(0, numIterations):
results = []
for j in range(len(train_elements)):
results.append(
knn.get_error_estimation_weighted_on_input(
train_elements[j].input, theta,
train_elements[j].neighbors_i,
train_elements[j].neighbors_o, k, False))
hypothesis = numpy.asarray(results)
loss = hypothesis - y
cost = numpy.sum(loss**2) / (2 * m)
if verbose:
Support.colored_print("Iteration %d | Cost: %f" % (i, cost), "red")
if jump_enabled:
if previous_cost == cost:
counter_for_jump += 1
if counter_for_jump > 10:
counter_for_jump = 0
if cost > 10:
# making jump
# selecting random indexes to perturbate
indexes_to_perturbate = numpy.random.choice(
range(len(theta)),
int(float(len(theta)) * 0.4),
replace=False)
for j in range(len(indexes_to_perturbate)):
# selecting random percentage perturbation
perturbation_value = random.randint(1, 6) * 0.1
perturbated = theta[
indexes_to_perturbate[j]] * perturbation_value
if random.randint(0, 2) == 0:
perturbated *= -1
theta[indexes_to_perturbate[j]] = perturbated
i -= 1
continue
else:
previous_cost = cost
# avg gradient per example
gradient = numpy.dot(x_trans, loss) / m
# update
theta = theta - alpha * gradient
cost = numpy.sum(loss**2) / (2 * m)
return theta, cost
#!/usr/bin/python
#coding=utf-8
#导入模块
import Support
#引用模块里的函数
Support.print_func("Test module.")
'''
Created on Mar 27, 2014
@author: Mark.E.Frymire
'''
import Support
Support.print_func("#1")
from Support import print_func
print_func("#2")
Money = 2000
print Money
def incrementMoney():
aLocalVar = "Hi, I'm a local string."
print "Locals:", locals()
print "Globals:", globals()
# Python assumes any variable assigned a value in a function is local, so you can't do this...
# Money = Money + 1
# We have to first specify that we're using the global version.
global Money
Money = Money + 1
incrementMoney()
print Money
# Use dir to get the names defined by a module
import math
my_game_tree[curr_node_id].print_node_details()
curr_gamestate = my_game_tree[curr_node_id].node_gamestate
empty_found = False
"""Find index of first empty (i.e. 0) in the current gamestate"""
for game_row_cntr in range(game_config.GAME_DIMENSION * game_config.GAME_DIMENSION):
for game_column_cntr in range(game_config.GAME_DIMENSION * game_config.GAME_DIMENSION):
if curr_gamestate[game_row_cntr][game_column_cntr] == 0:
empty_found = True
empty_row_idx = game_row_cntr
empty_col_idx = game_column_cntr
break
if empty_found:
break
"""get list of possible values for empty position"""
possible_vals = Support.compute_choices(curr_gamestate, empty_row_idx, empty_col_idx)
print(possible_vals)
"""check if any possible values returned"""
if len(possible_vals) > 0:
game_node_level = game_node_level + 1
print("New tree level:", game_node_level)
"""for each possible value , create a MCTS node with appropriate values"""
for new_val in possible_vals:
"""tmp_MCTSnode.clear_node()"""
print("New value:", new_val)
tmp_gamestate = curr_gamestate
tmp_gamestate[empty_row_idx][empty_col_idx] = new_val
game_node_count = game_node_count + 1
my_game_tree[curr_node_id].node_children.append(game_node_count)
my_game_tree.append(
MCTS_node.MCTSnode(