def view(self, factor=1., subset=None):
"""Start an animation of the mode. The displacements can be
scaled by a |factor| to make them better visible, and
a |subset| of the total system can be specified as well.
This function requires an external viewer, see module
Module:MMTK.Visualization for details."""
Visualization.viewMode(self, factor, subset)
def classifier_train_predict(X_train, y_train, X_test, y_test) :
print()
print('Running various classifiers to predict the labels of the test data...')
classifiers = {
"Baseline Classifier": DummyClassifier(strategy='most_frequent', random_state=0),
"Logistic Regression": LogisticRegression(),
"Linear SVM": SVC(),
"Non Linear SVM": SVC(kernel='rbf'),
"Gradient Boosting Classifier": GradientBoostingClassifier(n_estimators=100),
"Decision Tree": DecisionTreeClassifier(),
"Random Forest": RandomForestClassifier(n_estimators=100),
"Neural Network": MLPClassifier(alpha = 1),
"Naive Bayes": GaussianNB(),
"Decision tree" : DecisionTreeClassifier(criterion='entropy'),
"Kernelized SVM" : SVC(decision_function_shape='ovo'),
"AdaBoost": AdaBoostClassifier(),
"XGBoost" : XGBClassifier()
}
for i in classifiers :
clf = classifiers[i]
clf = clf.fit(X_train, y_train)
predicted = clf.predict(X_test)
print()
print (i," Accuracy Score: ",accuracy_score(y_test, predicted))
cnf_matrix = confusion_matrix(y_test, predicted)
print()
Visualization.plotConfusionMatrix(cnf_matrix, i)
def runAndSaveMultiple(run_amount):
for i in range(run_amount):
start = time.clock()
grid.clearGrid()
seed = i
random.seed(str(seed))
global img_no, nets_unsorted, index_path_dict, conn_per_chip, conn_free_per_chip, not_used_chips, \
not_layed_paths, path_lay_amount, visualise_dict, netlist_sorted, hillclimber_visualisation
img_no = 0
nets_unsorted = [] # List with start and end points of lines
index_path_dict = {} # Dictionary with net-index as key and the path as value
conn_per_chip = {} # Dictionary with the number of
conn_free_per_chip = {}
not_used_chips = []
not_layed_paths = []
path_lay_amount = {}
visualise_dict = {}
netlist_sorted = []
hillclimber_visualisation = [[], []]
paths = main()
if paths != []:
total_length = 0
for path in paths:
total_length += len(path) - 1
path_saver.saveToFile(paths, total_length, seed)
Visualization.hillclimberVisualisation(hillclimber_visualisation, seed)
print "Calculated in:", time.clock() - start
def mhSample(probabilityX, probabilityYOfX, sampleYFromX, x_initial, x_list,
sample_time, viz, *args):
'''initial: x_list = range(sample_time)'''
if len(args) == 1:
args = args[0]
x_old = x_initial
x_new = sampleYFromX(x_old, args)
alpha = computeAlpha(probabilityX, probabilityYOfX, x_old, x_new, args)
if np.log(np.random.uniform(0, 1)) < alpha:
received_x_new = x_new
else:
received_x_new = x_old
x_list[-sample_time] = received_x_new
sample_time = sample_time - 1
print sample_time, np.exp(alpha), received_x_new, x_new, x_old
if viz == 1:
# Visualization.plotValue(x_list[:-sample_time],'', 0, np.size(x_list,0), 0, 11)
# visual_list = np.sum(np.array(x_list[:-sample_time])*np.array([[1,20]]*len(x_list[:-sample_time])),1)
Visualization.plotHistgram(x_list[:-sample_time], 10, -1, 2, 0, 100)
if sample_time == 1:
if viz == 1:
Visualization.saveVis('masterchasing_hist.png')
return x_list
else:
return mhSample(probabilityX, probabilityYOfX, sampleYFromX,
x_list[-sample_time - 1], x_list, sample_time, viz,
args)
def plotPriceLabel(ticker, isGridSearch=True, isIndex=True):
if isIndex:
X_train, y_train, X_test, y_test = getXy(ticker,
isDrop=True,
featuresList=featuresList3,
dropList=dropList3)
else:
X_train, y_train, X_test, y_test = getXy(ticker,
isDrop=True,
featuresList=featuresList1,
dropList=dropList1)
[ticker, clf, accuracy, fscore, bestTrainParm,
predictions] = ml(SVM,
ticker,
X_train,
y_train,
X_test,
y_test,
isGridSearch=True,
parm=SVMParm2)
df = getStock(ticker)
startTestDate = dt.date(2016, 1, 1)
endTestDate = dt.date(2016, 12, 31)
df = df.ix[startTestDate:endTestDate]
df = df[['Adj Close']]
df['Prediction'] = predictions
df['Actual Trend'] = y_test
vs.closeLabel(df, ticker)
def optimize_angle(cylinder, seed, img):
# Calculating step size based on radius and height:
step_dec = math.degrees(2 * np.arcsin(cylinder.radius /
(2 * cylinder.height)))
mod90 = 90 % step_dec
mod360 = 360 % step_dec
div90 = 90 // step_dec
div360 = 360 // step_dec
step_psi = step_dec + mod90 / div90
step_theta = step_dec + mod360 / div360
fit_score = []
theta_arr = []
psi_arr = []
psi = 0
while psi <= 90:
theta = 0
if psi == 0: # Don't need to rotate if vertical
cropped_img = mask_dataset(cylinder, seed, img)
score = score_fit(cylinder, cropped_img, translated=False)
vis.visualise_cylinder(str(score) + ' theta ' + str(theta) +
' psi ' + str(psi) + '.tif',
img,
cylinder,
seed,
translated=False)
fit_score.append(score)
theta_arr.append(theta)
psi_arr.append(psi)
else:
while theta < 360:
cylinder.rotate(theta, psi)
cropped_img = mask_dataset(cylinder, seed, img)
score = score_fit(cylinder, cropped_img, translated=True)
vis.visualise_cylinder(str(score) + ' theta' + str(theta) +
' psi ' + str(psi) + '.tif',
img,
cylinder,
seed,
translated=True)
fit_score.append(score)
theta_arr.append(theta)
psi_arr.append(psi)
theta = step_theta + theta
psi = step_psi + psi
best_score = max(fit_score)
high_score_index = fit_score.index(best_score)
theta = theta_arr[high_score_index]
psi = psi_arr[high_score_index]
cylinder.rotate(theta, psi)
return best_score, theta, psi
def __import_fuel_map(self):
user_settings = UserSettings()
file_filter = 'Ascii file (*' + AsciiParser.FILE_EXT + ')'
file, filt = QFileDialog.getOpenFileName(self, 'Open File', user_settings.working_dir, file_filter)
if file:
# FIXME: increase SIZE when there are lots of cells in fuel map and ignition
qApp.setOverrideCursor(Qt.WaitCursor)
try:
new_editor = FuelMapViewer(self, file)
except IndexError:
qApp.restoreOverrideCursor()
QMessageBox.information(self, "Invalid file", "A problem occurred while loading the fuel map. Please "
"verify that the fuel map does not contain non-integer "
"numbers")
return
if self._fl_map_editor:
self._fl_map_editor.deleteLater()
self._fl_map_editor = new_editor
self._fl_map_editor.setEnabled(True)
self.__setup_fl_map_lgnd()
# Enable relevant widgets
self.action_export_fuel_map.setEnabled(True)
# This means that a DEM has already been loaded,
# so the user can now convert to FDS file
if self._ign_pt_editor:
self.__init_sim_settings()
self.action_create_environment.setEnabled(True)
if self._visualization:
self._visualization.deleteLater()
self._visualization = Visualization(self._fl_map_editor.parser(), self._ign_pt_editor.parser(), self)
self._visualization.setEnabled(True)
self._visualization.hide()
# Set current tab to fuel type legend
self._tab_widget.setCurrentIndex(1)
self._fm_title_label.setText("Fuel Map Title: " + util.get_filename(file))
# Tab index might not change, so __tab_changed will never get called
self._fl_map_editor.show()
qApp.restoreOverrideCursor()
def runMain():
time_start = time.clock()
path_list = main()
time_end = time.clock()
path_length = 0
for index, path in enumerate(path_list):
path_list[index] = superSmoothPath(path)
path_length += len(path) - 1
print "Path length:", path_length
print "Calculated in:", int(time_end - time_start), "seconds"
Visualization.runVisualization(path_list)
Visualization.run3DVisualisation(path_list, 0)
def tuneSVC(X_train_selected, y_train, X_test_selected, y_test):
print()
print('SVC gives better accuracy as compared to other classifiers, tuning hyperparameters of SVC...')
print()
param = svc_param_selection(X_train_selected, y_train, 3)
model = svm.SVC(C=param['C'], kernel= 'rbf', gamma=param['gamma'])
model = model.fit(X_train_selected, y_train)
predicted = model.predict(X_test_selected)
print()
print("Accuracy Score of SVC with hyperparameters tuned: ",accuracy_score(y_test, predicted))
cnf_matrix = confusion_matrix(y_test, predicted)
print()
Visualization.plotConfusionMatrix(cnf_matrix, 'Tuned SVC')
def analyze_data(time_interval=TimeInterval, refined_type=FullyPreprocessedPath):
print 'time_interval: ' + str(time_interval) + ' min'
print 'refined_type: ' + refined_type
print '--------------------------------------------'
# Refine the data and save
refined_data_path = Preprocess.preprocess_data(time_interval, refined_type)
# Build similarity model and save
Similarity.Build.similarity_model(time_interval, refined_type)
# Set data for visualization
Visualization.set_data4visualization(time_interval, refined_type)
def checkPathDict(path_dict, iteration):
points_occupied = []
paths = path_dict.keys()
for path in paths:
for point in path_dict[path]:
if point in points_occupied and point not in chips:
print "Point", point
print "Path no", path
print "Iteration", iteration
Visualization.runVisualization(path_dict.values())
raise StandardError
else:
points_occupied.append(point)
def cluster_analysis(
PosData,
ion_types=['Ranged'],
method='OPTICS-APT',
eps=2.0,
minpts=10,
min_node_size=None,
significant_separation=0.75,
k=None,
node_similarity=0.9,
cluster_member_prob=0.5, # from here are experts
est_bg=None,
min_cluster_size=None, # here background estimation could be added in future
save_file=True,
show_visual=False,
show_background=False): # here just to control file and visual output
init_time = time.time()
Clusterer = OPTICSAPT(PosData)
Clusterer.ion_selection(ion_types)
if method == 'DBSCAN':
Clusterer.DBSCAN_clustering(eps, minpts)
elif method == 'OPTICS-APT':
Clusterer.do_optics(eps, minpts)
Clusterer.hierarchy_clustering(
min_node_size=min_node_size,
significance_of_separation=significant_separation,
k=k,
similarity_level=node_similarity,
cluster_member_prob=cluster_member_prob)
Clusterer.create_clusters(est_bg=est_bg,
min_cluster_size=min_cluster_size)
if save_file:
Clusterer.write_RD_to_file(output_filename + '_ol_RD_CD')
if save_file:
Clusterer.cluster_stats(output_filename + '_cluster_stats')
Clusterer.write_cluster_to_file(output_filename + '_clusters')
Clusterer.write_indexed_cluster_rrng(output_filename + '_clusters')
Clusterer.write_log(output_filename + '_log')
fin_time = time.time()
print('total computation time is: ', fin_time - init_time)
if show_visual:
visual.visualization(Clusterer, background=show_background)
return Clusterer
def runTest():
start = time.clock()
#path = aStarPathFinder((1, 1, 0), (15, 8, 0))
path = [(1, 1, 0), (1, 2, 0), (1, 3, 0), (1, 3, 1), (1, 4, 1), (1, 5, 1), (2, 5, 1), (3, 5, 1), (3, 5, 0), (3, 6, 0), (4, 6, 0), (5, 6, 0), (5, 7, 0), (5, 8, 0), (5, 8, 1), (4, 8, 1), (4, 7, 1), (4, 7, 2), (5, 7, 2), (6, 7, 2), (7, 7, 2), (7, 7, 1), (7, 8, 1), (8, 8, 1), (8, 9, 1), (8, 9, 0), (9, 9, 0), (10, 9, 0), (10, 8, 0), (10, 7, 0), (10, 6, 0), (11, 6, 0), (12, 6, 0), (12, 7, 0), (12, 8, 0), (13, 8, 0), (14, 8, 0), (15, 8, 0)]
end = time.clock()
print "Path calculate time", end - start
print "Path length: ", len(path)
Visualization.run3DVisualisation([path], 0)
start = time.clock()
smoother_path = smoothPath(path)
end = time.clock()
print "Smooth in:", end - start
Visualization.run3DVisualisation([smoother_path], 0)
def mask_3d_array(array):
print("masking array")
result = []
for i in range(len(array)):
print(f"masking slice {i + 1}/{len(array)}")
slice = np.squeeze(array)[:][:][i]
slice_mask = Visualization.make_lungmask(slice)
masked_slice = Visualization.apply_lungmask(slice, slice_mask)
result.append(masked_slice)
result = np.asarray(result)
print("masking done")
return result
def votingClassifier(X_train, y_train, X_test, y_test):
clf1 = RandomForestClassifier(n_estimators=50)
clf2 = SVC(kernel = 'rbf')
clf3 = SVC()
print()
print('Voting Classifier with hard voting:')
vote_model = VotingClassifier(estimators=[('Random', clf1), ('kernelized', clf2), ('SVC', clf3)], voting='hard')
vote_model.fit(X_train,y_train)
y_pred = vote_model.predict(X_test)
print()
print("Accuracy Score of Voting Classifier: ",accuracy_score(y_test, y_pred))
cnf_matrix = confusion_matrix(y_test, y_pred)
print()
Visualization.plotConfusionMatrix(cnf_matrix, 'voting classifier')
def main():
Settings.init()
default_radius = 2
default_height = 5
# Load in image and seeds
filename = 'testdata.tif'
img = tif.imread(filename)
seedfilename = 'testdata_maxima_binary.tif'
seeds = s.get_seeds(seedfilename)
cylinder = cyl.Cylinder(default_radius, default_height)
vis.render_gauss(cylinder)
best_score, best_theta, best_psi = Optimize.optimize_angle(cylinder, seeds[257], img)
def open_visualisation(self, event):
import Visualization
# dlg = tk.Toplevel(self.master)
r = tk.Tk()
dialog = Visualization.Visualization(r)
dialog.fill_combobox1()
dialog.run()
def average_over_seeds(model_type_list,
model_parameters_list,
n=N,
k=K,
t=T,
possible_rewards=POSSIBLE_REWARDS,
get_reward_probabilities=get_reward_probabilities,
min_seed=MIN_SEED,
max_seed=MAX_SEED):
"""
run simulation for many models, with different seeds and return the required arrays for Visualization.py
plot functions with vis.DATA list_type argument
:param model_type_list: list of ModelType enums, containing the models to run
:param model_parameters_list: list of dictionaries containing parameters for the models in model_type_list
:param n: number of machines
:param k: number of machines to choose each round
:param t: number of trials
:param possible_rewards: list of possible machine rewards
:param get_reward_probabilities: function that returns a list of reward probabilities
:param min_seed: lowest seed to run
:param max_seed: highest seed to run
:return: convergence, reward_sum, distance_from_real_distributions - arrays of tuples, first argument in tuple
is the sim.type and the second is the actual data
"""
convergence_list = np.zeros((len(model_type_list), t - 1))
reward_sums = np.zeros((len(model_type_list), t))
regrets = np.zeros((len(model_type_list), t))
distances = [[] for _ in range(len(model_type_list))]
sim_titles = []
for seed in tqdm(range(min_seed, max_seed + 1)):
optimal_reward = None
cur_rewards = np.zeros_like(reward_sums)
for i, model_type, model_parameters in tqdm(
zip(np.arange(len(model_type_list)), model_type_list,
model_parameters_list)):
np.random.seed(seed)
sim = s.Simulation(n, k, t, possible_rewards,
get_reward_probabilities, model_type,
**model_parameters)
if seed == min_seed:
sim_titles.append(sim.type)
sim.run_simulation()
convergence_list[i, :] += sim.get_convergence_rate()
if sim.type == "Optimal Model":
optimal_reward = sim.get_reward_sum()
cur_rewards[i, :] += sim.get_reward_sum()
reward_sums[i, :] += cur_rewards[i, :]
for j, machine in enumerate(sim.machine_list):
distances[i].append(
vis.fr_metric(
machine.reward_probabilities,
sim.model.estimated_machine_reward_distribution[j, :]))
regrets[...] += optimal_reward - cur_rewards
convergence_list /= (max_seed - min_seed + 1)
reward_sums /= (max_seed - min_seed + 1)
regrets /= (max_seed - min_seed + 1)
return [(sim_titles[i], convergence_list[i, :]) for i in range(len(model_type_list))], \
[(sim_titles[i], reward_sums[i, :]) for i in range(len(model_type_list))], \
[(sim_titles[i], distances[i]) for i in range(len(model_type_list))], \
[(sim_titles[i], regrets[i]) for i in range(len(model_type_list))]
class TestTrialResponse(unittest.TestCase):
@data(('0.pkl',
[50,11,3.3,1.83,0.92,0.31],
12,
36,
4.0,
0.0,
0.7,
0.0,
8,
Visualization.Visualize(circleSize=10, screenColor=[255,255,255], screen = pg.display.set_mode([800,800]),
saveImage=False, saveImageFile='image'),
0.95,
{50:5,11:30,3.3:60,1.83:90,0.92:120,0.31:150}))
@unpack
def testResponseForSimpleChasing(self,filename,subtletyHypothesis,updateFrequency,attentionSwitchFrequency,precisionPerSlot,precisionForUntracked,memoryratePerSlot,memoryrateForUntracked,attentionLimitation,visualize,responseRule,precisionToSubtletyDict):
loadTrajectory=LoadTrajectory.loadTrajectory
initialPrior=targetCode.initialPrior(attentionLimitation)
computePosterior=calPosterior.calPosteriorLog
attention=Attention.AttentionToPrecisionAndDecay(precisionPerSlot, precisionForUntracked, memoryratePerSlot, memoryrateForUntracked)
attentionSwitch=Attention.AttentionSwitch(attentionLimitation)
perception=Perception.Perception(attention, computePosterior, attentionSwitch, attentionSwitchFrequency)
response=Response.RuleBasedResponse(responseRule, precisionToSubtletyDict)
trial=targetCode.Trial(subtletyHypothesis, updateFrequency, loadTrajectory, visualize, initialPrior, response, perception)
trialResponse=trial(filename)
# self.assertTrue(trialResponse['action'])
self.assertLessEqual(trialResponse['RT'],8000)
self.assertEqual(trialResponse['wolfIdentity'],0)
self.assertEqual(trialResponse['sheepIdentity'],1)
def analyze_data(time_interval=TimeInterval, refined_type=FullyPreprocessedPath):
print 'time_interval: ' + str(time_interval) + ' min'
print 'refined_type: ' + refined_type
print '--------------------------------------------'
# Draw graphs and save the figures
graph_directory = Graph.Save.raw_data2graph()
# Refine the data and save
refined_data_path = Preprocess.refining_data(time_interval, refined_type)
# Build similarity model and save
Similarity.Build.similarity_model(time_interval, refined_type)
# Set data for visualization
Visualization.set_data4visualization(time_interval, refined_type)
def edit_list(dataframe, playlist_ids, mapping):
dataframe = pd.read_json(dataframe)
print('playlist_ids' + str(playlist_ids))
print("Pl_name_Dict" + str(mapping))
adding = playlist_ids[1]
new_spec = playlist_ids[0]
pl_name_dict = mapping[1]
new_list = [
html.Div([
dcc.Checklist(id={
"index": i,
"type": "done"
},
options=[{
"label": "",
"value": "done"
}],
value=done,
style={"display": "inline"},
labelStyle={"display": "inline"}),
html.Div((lambda x: pl_name_dict[x]
if x in pl_name_dict.keys() else x)(text),
id={"index": i},
style=style_done if done else style_todo)
],
style={"clear": "both"})
for i, (text, done) in enumerate(new_spec)
]
radar_graph = get_radar_graph(dataframe)
bar_graph = Visualization.make_bar_graph(dataframe)
y = [new_list, adding, radar_graph, bar_graph]
#print(y)
return y
def visualise_pos_neg_words():
rule_word_dict = vn.visualize(emotion_words, sentiment_words, file_name)
e_pos_words = get_words_from_emotion_list(rule_word_dict['e_pos'])
s_pos_words = get_words_from_emotion_list(rule_word_dict['s_pos'])
e_neg_words = get_words_from_emotion_list(rule_word_dict['e_neg'])
s_neg_words = get_words_from_emotion_list(rule_word_dict['s_neg'])
pos_words = list(set(e_pos_words + s_pos_words))
neg_words = list(set(e_neg_words + s_neg_words))
final_neg_words = []
for wo in neg_words:
if wo in pos_words:
if wo in e_neg_words and wo in s_neg_words:
final_neg_words.append(wo)
else:
final_neg_words.append(wo)
final_pos_words = []
for wo in pos_words:
if wo not in final_neg_words:
final_pos_words.append(wo)
return {
'popular_words': final_pos_words,
'non_popular_words': final_neg_words
}
def __import_dem(self):
user_settings = UserSettings()
file_filter = 'Ascii file (*' + AsciiParser.FILE_EXT + ')'
file, filt = QFileDialog.getOpenFileName(self, 'Open File',
user_settings.working_dir,
file_filter)
if file:
qApp.setOverrideCursor(Qt.WaitCursor)
if self._ign_pt_editor:
self._ign_pt_editor.deleteLater()
self._ign_pt_editor = IgnitionPointViewer(self, file)
self._ign_pt_editor.setEnabled(True)
self._setup_ign_pt_map_lgnd()
# Enable relevant widgets
self.action_export_dem.setEnabled(True)
# This means that a fuel map has already been loaded,
# so the user can now convert to FDS file
if self._fl_map_editor:
self.__init_sim_settings()
self.action_create_environment.setEnabled(True)
if self._visualization:
self._visualization.deleteLater()
self._visualization = Visualization(
self._fl_map_editor.parser(), self._ign_pt_editor.parser(),
self)
self._visualization.setEnabled(True)
self._visualization.hide()
# Set current tab to fuel type legend
self._tab_widget.setCurrentIndex(2)
self._dem_title_label.setText("DEM Title: " +
util.get_filename(file))
self._ign_pt_editor.show()
qApp.restoreOverrideCursor()
def sampling_def(image1, dist_img, threshold, Sample_Density):
Samples2 = SpatialSampling.DiskSamples(image1, dist_img, threshold)
Samples2.GenSamples(
Sample_Density,
80000) # This distance will be used to calculate strains
point_arr2 = Samples2.samples
sample_point2 = np.transpose(point_arr2)
Visualization.DataVisulization(image1, threshold).scatterplot(point_arr2)
return sample_point2
def plotPriceLabel():
ticker = 'MMM'
X_train, y_train, X_test, y_test = getXy(ticker,
isDrop=True,
predict_period=15)
[clf_Name, clf] = SVM(X_train, y_train, isGridSearch=True)
predictions = clf.predict(X_test)
df = getStock(ticker)
startTestDate = dt.date(2016, 1, 1)
endTestDate = dt.date(2016, 12, 31)
df = df.ix[startTestDate:endTestDate]
df = df[['Adj Close']]
df['Prediction'] = predictions
vs.closeLabel(df)
def runMain():
start = time.clock()
paths = main()
print "Calculated in:", time.clock() - start
if paths == []:
print "Could not finish in given number of iterations"
else:
print "Amount of paths", len(paths)
total_length = 0
for path in paths:
total_length += len(path) - 1
print "Total length:", total_length
print "Not layed paths", not_layed_paths
if not_used_chips != []:
print "Deleted chips:", not_used_chips
print paths
Visualization.run3DVisualisation(paths)
Visualization.runVisualization(paths)
def showPath(path, graph, ranges=[]):
edgesToHighlight = []
visitedEdge = dict()
for node in graph.nodes():
for neighbour in list(graph.neighbors(node)):
for level in list(graph[node][neighbour]):
visitedEdge[(node, neighbour, level)] = False
number = 1
for id in range(1, len(path)):
level = 0
while visitedEdge[((path[id - 1], path[id], level))]:
level += 1
visitedEdge[((path[id - 1], path[id], level))] = True
edgesToHighlight.append((path[id - 1], path[id], level))
vis.draw(graph, edgesToHighlight, True, ranges, number)
number += 1
def question3():
rate = 0.00005
count = 0
con_ws = Perceptrons.Weights([-1, 0, 0.5, -0.5, 0.5], rate)
cla_ws = Perceptrons.Weights([-1.101, -0.008, 0.652, -0.372, 0.412], rate)
conf = []
classf = []
col = []
for sample in data:
if con_ws.activation(sample) == sample[-1]:
count += 1
col.append('g')
else:
col.append('r')
conf.append(round(con_ws.result, 3))
cla_ws.activation(sample)
classf.append(round(cla_ws.result, 3))
Visualization.confidence(conf, classf, col)
print(count / len(data))
def question1():
ws = []
for rate in [0.005, 0.001, 0.00001]:
Perceptrons.initalweights = [-1, 1, 1, 1, 1]
accuracy, arr = Perceptrons.crossvalidation(data, 10, rate)
ws.append(arr)
print("learning rate: ", rate)
print("accuracy: ", accuracy)
print("weights:", arr, '\n')
Visualization.RatesComparsion(ws)
def view(self, configuration=None, format='pdb'):
"""Starts an external viewer for the object in the given
|configuration|. The optional parameter |format| indicates
which format (and hence which viewer) should be used;
the formats are "pdb" and "vrml". An optional subformat
specification can be added to the format name, separated
by a dot. The subformats of "pdb" are defined by the
module 'Scientific.IO.PDB', the subformats of "vrml" are
"wireframe" (the default, yielding a wireframe representation),
"ball_and_stick" (yielding a ball-and-stick representation),
"highlight" (like wireframe, but with a small sphere for
all atoms that have an attribute "highlight" with a non-zero value),
and "charge" (wireframe plus small spheres for the atoms with colors
from a red-to-green color scale to indicate the charge)."""
universe = self.universe()
if universe is not None:
configuration = universe.contiguousObjectConfiguration(
[self], configuration)
Visualization.viewConfiguration(self, configuration, format)
def auto(tiss, data="Female"):
print('\n')
segmentation, dico = getDSubstance(data, tiss)
dicomdir = segmentation.dicomdir
print('Dicom Dir : ', dicomdir)
print('Initialize ImageDicom')
image = segmentation.dicomimage
if "box" in dico.keys():
image.cropBoxImages(dico["box"]["dheight"], dico["box"]["drow"],
dico["box"]["dcolumn"])
segmentation.data_dico[segmentation.name]["box"] = dico["box"]
print("height :", image.height)
segmentation.pipeline()
print('Initialize Visualization')
myMesh = Visualization(segmentation)
myMesh.pipeline()
print('Object Created')
print('----------')
print('\n')
def view(self, configuration = None, format = 'pdb'):
"""Starts an external viewer for the object in the given
|configuration|. The optional parameter |format| indicates
which format (and hence which viewer) should be used;
the formats are "pdb" and "vrml". An optional subformat
specification can be added to the format name, separated
by a dot. The subformats of "pdb" are defined by the
module 'Scientific.IO.PDB', the subformats of "vrml" are
"wireframe" (the default, yielding a wireframe representation),
"ball_and_stick" (yielding a ball-and-stick representation),
"highlight" (like wireframe, but with a small sphere for
all atoms that have an attribute "highlight" with a non-zero value),
and "charge" (wireframe plus small spheres for the atoms with colors
from a red-to-green color scale to indicate the charge)."""
universe = self.universe()
if universe is not None:
configuration = universe.contiguousObjectConfiguration([self],
configuration)
Visualization.viewConfiguration(self, configuration, format)
def Update(Bodies, Steps=100, Snaps=10, L=3, njobs=1, Plots=False, direct=''):
'''
This function updates the system.
In Args:
- Bodies: Array containing the bodies to be updated.
- *Steps: (Optional) The number of update steps. If not given, it will update 100 steps.
- *Snaps: (Optional) The number of snapshots to take. This will only be useful when Plots = True.
- *L = 3 The scale of the system. Default is 3 AU.
- *Plots (Optional) If true, will save certain stapshots on the given directory.
- *direct (Needed if Plots = True) A string with the Path where you want to save the outputs.
- *njobs: (Optional) The number of cores to be used during the computation. By default is 1
i.e. the program will run sequentially.
Out Args:
- Bodies: Array containing the updated bodies.
'''
j = 0 # This is a counter for the number of snapshots.
for k in tqdm(range(Steps)):
time.sleep(0.01)
if Plots == True:
N_steps_snapshot = int(Steps / Snaps)
if k % N_steps_snapshot == 0: # This will plot only the necesary steps.
Visualization.Plot(
Bodies, k, j, L, direct
) # This will make a plot of the actual step of the simulation.
j += 1
B = Bodies # This is a "temporal array" that will serve to compute the acceleration in parallel
# without updating the positions of the bodies before we compute all the accelerations.
Parallel(n_jobs=njobs)(delayed(Compute_Accel)(i, B) for i in Bodies)
for i in range(len(Bodies)):
Bodies[i].velocity = Bodies[i].Compute_velocity()
Bodies[i].position = Bodies[i].Compute_position()
# Once the main parameters have been updated we define the acceleration (i) equal to the
# computed acceleration (i+1).
Bodies[i].acceleration_i = Bodies[i].acceleration_i_1
return Bodies
def question2():
Perceptrons.epochs = 20
ys = []
for rate in [0.005, 0.001, 0.00001]:
print("learning rate: ", rate)
Perceptrons.count = 0
Perceptrons.train_errors = []
Perceptrons.initalweights = [-1, 1, 1, 1, 1]
accuracy, arr = Perceptrons.crossvalidation(data, 10, rate)
print(Perceptrons.train_errors, '\n')
ys.append(Perceptrons.train_errors)
Visualization.AccuracyInEpochs(ys, 20)
def performKMeans(inputDataClass, k, mode, num_runs, visualize=False):
covar = -1
if mode == 3:
covar = performanceAnalyser.getFullCovariance(
inputDataClass.Train[:, :-1])
labels, means, rms, Ypred = kmeans.kfit(inputDataClass.Train[:, :-1],
k,
inputDataClass.Train[:, -1],
inputDataClass.Test[:, :-1],
num_runs=num_runs,
mode=mode,
covar=covar)
print("rms = " + str(rms))
print("Kmeans done")
Ytrue = inputDataClass.Test[:, -1]
print("Testing Accuracy = " +
str(performanceAnalyser.calcAccuracyTotal(Ypred, Ytrue)))
if visualize:
Visualization.visualizeKMeans(inputDataClass.Train[:, :-1], labels, k)
print("Kmeans visualized")
return Ytrue, Ypred
def sampling_def(image1, dist_img, threshold):
"""
this is the sampling function
input:
image1 --- (N,d) np.array
dist_img --- (N,d) np.array
threshold --- a float value
output:
sample_point2 ---(N,3) np.array
"""
Samples2 = SpatialSampling.DiskSamples(image1, dist_img, threshold)
Samples2.GenSamples(3, 80000) # this number controls the density
point_arr2 = Samples2.samples
sample_point2 = np.transpose(point_arr2)
Visualization.DataVisulization(image1, threshold).scatterplot(point_arr2)
return sample_point2
def get_radar_graph(data):
#global data
# print("Valid data"+ str(valid_data))
# print("Current ids" + str(current_ids))
# if len(filter) > 0:
# data = PlaylistRetriever.get_user_playlists(filter)
# else:
# data = PlaylistRetriever.get_user_playlists(current_ids)
print("got here")
fig = Visualization.make_radar_chart(data)
fig.update_layout(margin=dict(l=100, r=0, t=0, b=0),
#paper_bgcolor="LightSteelBlue"
)
fig.update_layout(legend=dict(
yanchor="top",
#y=0.99,
xanchor="left",
#x=0.01
))
return fig
shortest_paths = {path_number: [] for path_number in range(len(netlist))} # shortest_paths2 = [[(2, 10, 0), (2, 9, 0), (2, 8, 0)], [(12, 3, 0), (11, 3, 0), (10, 3, 0), (9, 3, 0), (9, 4, 0), (8, 4, 0)], [(8, 4, 0), (8, 3, 0), (8, 2, 0), (8, 2, 1), (7, 2, 1), (6, 2, 1), (5, 2, 1), (4, 2, 1), (3, 2, 1), (3, 2, 0)], [(16, 7, 0), (15, 7, 0), (15, 6, 0), (15, 6, 1), (14, 6, 1), (14, 6, 2), (14, 6, 3), (14, 6, 4), (13, 6, 4), (12, 6, 4), (11, 6, 4), (10, 6, 4), (9, 6, 4), (8, 6, 4), (7, 6, 4), (6, 6, 4), (5, 6, 4), (5, 5, 4), (5, 4, 4), (4, 4, 4), (4, 3, 4), (3, 3, 4), (2, 3, 4), (1, 3, 4), (0, 3, 4), (0, 3, 3), (0, 3, 2), (0, 3, 1), (0, 3, 0), (0, 2, 0), (1, 2, 0), (1, 1, 0)], [(3, 2, 0), (3, 3, 0), (3, 3, 1), (3, 3, 2), (3, 4, 2), (3, 4, 3), (3, 4, 4), (3, 5, 4), (4, 5, 4), (4, 6, 4), (4, 6, 3), (4, 7, 3), (5, 7, 3), (6, 7, 3), (7, 7, 3), (8, 7, 3), (9, 7, 3), (10, 7, 3), (10, 7, 2), (11, 7, 2), (12, 7, 2), (12, 7, 1), (13, 7, 1), (13, 7, 0)], [(2, 8, 0), (2, 7, 0), (1, 7, 0), (0, 7, 0), (0, 6, 0), (0, 6, 1), (0, 5, 1), (0, 5, 2), (1, 5, 2), (1, 5, 3), (1, 4, 3), (1, 3, 3), (2, 3, 3), (2, 2, 3), (2, 2, 2), (2, 1, 2), (2, 0, 2), (2, 0, 1), (2, 0, 0), (3, 0, 0), (4, 0, 0), (5, 0, 0), (6, 0, 0), (6, 1, 0)], [(1, 5, 0), (1, 6, 0), (2, 6, 0), (3, 6, 0), (3, 6, 1), (3, 5, 1), (3, 4, 1), (4, 4, 1), (5, 4, 1), (6, 4, 1), (7, 4, 1), (8, 4, 1), (8, 4, 0)], [(1, 5, 0), (2, 5, 0), (2, 5, 1), (2, 5, 2), (3, 5, 2), (3, 5, 3), (4, 5, 3), (5, 5, 3), (6, 5, 3), (7, 5, 3), (8, 5, 3), (9, 5, 3), (10, 5, 3), (10, 5, 4), (11, 5, 4), (12, 5, 4), (13, 5, 4), (14, 5, 4), (14, 5, 3), (15, 5, 3), (15, 5, 2), (15, 5, 1), (15, 5, 0), (16, 5, 0)], [(12, 3, 0), (12, 4, 0), (11, 4, 0), (10, 4, 0), (10, 4, 1), (10, 4, 2), (9, 4, 2), (8, 4, 2), (7, 4, 2), (7, 5, 2), (7, 5, 1), (7, 6, 1), (7, 7, 1), (7, 8, 1), (6, 8, 1), (6, 8, 0)], [(2, 8, 0), (3, 8, 0), (3, 7, 0), (4, 7, 0), (5, 7, 0), (5, 6, 0), (6, 6, 0), (7, 6, 0), (7, 7, 0), (7, 8, 0), (8, 8, 0), (9, 8, 0)], [(1, 5, 0), (1, 4, 0), (1, 3, 0), (2, 3, 0), (2, 2, 0), (3, 2, 0)], [(6, 1, 0), (7, 1, 0), (7, 2, 0), (7, 3, 0), (7, 4, 0), (8, 4, 0)], [(15, 1, 0), (15, 0, 0), (15, 0, 1), (15, 0, 2), (14, 0, 2), (13, 0, 2), (12, 0, 2), (11, 0, 2), (10, 0, 2), (9, 0, 2), (8, 0, 2), (7, 0, 2), (6, 0, 2), (5, 0, 2), (4, 0, 2), (4, 1, 2), (4, 2, 2), (4, 3, 2), (4, 4, 2), (4, 5, 2), (4, 5, 1), (4, 5, 0)], [(16, 5, 0), (16, 4, 0), (16, 3, 0), (16, 2, 0), (16, 2, 1), (15, 2, 1), (15, 2, 2), (14, 2, 2), (14, 2, 3), (13, 2, 3), (12, 2, 3), (11, 2, 3), (11, 2, 2), (11, 2, 1), (11, 2, 0), (12, 2, 0)], [(4, 5, 0), (5, 5, 0), (6, 5, 0), (7, 5, 0), (8, 5, 0), (8, 4, 0)], [(12, 11, 0), (12, 10, 0), (12, 9, 0), (13, 9, 0), (14, 9, 0), (15, 9, 0), (16, 9, 0), (17, 9, 0), (17, 8, 0), (17, 7, 0), (17, 6, 0), (17, 5, 0), (16, 5, 0)], [(1, 11, 0), (1, 12, 0), (2, 12, 0), (3, 12, 0), (4, 12, 0), (5, 12, 0), (6, 12, 0), (7, 12, 0), (8, 12, 0), (9, 12, 0), (10, 12, 0), (11, 12, 0), (12, 12, 0), (12, 11, 0)], [(1, 1, 0), (1, 1, 1), (1, 2, 1), (1, 3, 1), (1, 4, 1), (2, 4, 1), (2, 4, 0), (3, 4, 0), (3, 5, 0), (4, 5, 0)], [(6, 1, 0), (5, 1, 0), (4, 1, 0), (4, 2, 0), (3, 2, 0)], [(1, 9, 0), (1, 9, 1), (1, 9, 2), (1, 9, 3), (2, 9, 3), (3, 9, 3), (4, 9, 3), (4, 9, 2), (5, 9, 2), (6, 9, 2), (7, 9, 2), (8, 9, 2), (9, 9, 2), (9, 8, 2), (10, 8, 2), (11, 8, 2), (11, 8, 1), (11, 8, 0)], [(2, 10, 0), (2, 11, 0), (3, 11, 0), (4, 11, 0), (5, 11, 0), (5, 11, 1), (6, 11, 1), (7, 11, 1), (8, 11, 1), (9, 11, 1), (10, 11, 1), (10, 10, 1), (10, 9, 1), (11, 9, 1), (12, 9, 1), (12, 8, 1), (13, 8, 1), (14, 8, 1), (15, 8, 1), (15, 8, 0)], [(6, 8, 0), (6, 7, 0), (6, 7, 1), (6, 6, 1), (6, 6, 2), (6, 5, 2), (6, 4, 2), (6, 3, 2), (6, 2, 2), (6, 1, 2), (7, 1, 2), (7, 1, 1), (8, 1, 1), (8, 1, 0), (9, 1, 0), (10, 1, 0)], [(9, 10, 0), (8, 10, 0), (7, 10, 0), (7, 10, 1), (6, 10, 1), (5, 10, 1), (4, 10, 1), (3, 10, 1), (3, 9, 1), (3, 9, 2), (2, 9, 2), (2, 8, 2), (2, 8, 3), (2, 7, 3), (2, 6, 3), (2, 5, 3), (2, 4, 3), (2, 4, 2), (2, 3, 2), (2, 3, 1), (2, 2, 1), (2, 1, 1), (2, 1, 0), (1, 1, 0)], [(14, 2, 0), (14, 2, 1), (14, 1, 1), (14, 0, 1), (14, 0, 0), (13, 0, 0), (12, 0, 0), (11, 0, 0), (10, 0, 0), (10, 1, 0)], [(10, 1, 0), (10, 1, 1), (10, 2, 1), (10, 3, 1), (11, 3, 1), (11, 4, 1), (12, 4, 1), (12, 5, 1), (13, 5, 1), (13, 6, 1), (13, 6, 0), (13, 7, 0)], [(16, 7, 0), (16, 6, 0), (16, 5, 0)], [(10, 1, 0), (10, 2, 0), (9, 2, 0), (9, 2, 1), (9, 3, 1), (9, 4, 1), (9, 5, 1), (10, 5, 1), (10, 6, 1), (10, 7, 1), (10, 8, 1), (10, 8, 0), (11, 8, 0)], [(13, 7, 0), (12, 7, 0), (12, 6, 0), (12, 6, 1), (12, 6, 2), (12, 6, 3), (11, 6, 3), (10, 6, 3), (9, 6, 3), (8, 6, 3), (7, 6, 3), (6, 6, 3), (5, 6, 3), (5, 6, 2), (5, 5, 2), (5, 4, 2), (5, 3, 2), (5, 2, 2), (5, 1, 2), (5, 1, 1), (6, 1, 1), (6, 1, 0)], [(2, 8, 0), (2, 8, 1), (2, 9, 1), (2, 10, 1), (2, 11, 1), (2, 12, 1), (3, 12, 1), (4, 12, 1), (5, 12, 1), (6, 12, 1), (7, 12, 1), (8, 12, 1), (9, 12, 1), (10, 12, 1), (11, 12, 1), (11, 11, 1), (12, 11, 1), (12, 11, 0)], [(1, 1, 0), (0, 1, 0), (0, 1, 1), (0, 1, 2), (1, 1, 2), (1, 1, 3), (2, 1, 3), (3, 1, 3), (3, 2, 3), (3, 3, 3), (4, 3, 3), (5, 3, 3), (6, 3, 3), (7, 3, 3), (8, 3, 3), (8, 3, 2), (9, 3, 2), (10, 3, 2), (11, 3, 2), (11, 4, 2), (11, 5, 2), (11, 5, 1), (11, 5, 0)], [(12, 2, 0), (12, 3, 0)], [(15, 1, 0), (14, 1, 0), (13, 1, 0), (12, 1, 0), (11, 1, 0), (10, 1, 0)], [(15, 8, 0), (16, 8, 0), (16, 8, 1), (17, 8, 1), (17, 7, 1), (17, 6, 1), (17, 5, 1), (17, 4, 1), (17, 4, 0), (17, 3, 0), (17, 2, 0), (17, 1, 0), (16, 1, 0), (15, 1, 0)], [(6, 1, 0), (6, 2, 0), (5, 2, 0), (5, 3, 0), (4, 3, 0), (4, 4, 0), (4, 5, 0)], [(15, 8, 0), (14, 8, 0), (13, 8, 0), (13, 7, 0)], [(11, 5, 0), (10, 5, 0), (9, 5, 0), (9, 6, 0), (8, 6, 0), (8, 7, 0), (8, 7, 1), (8, 8, 1), (8, 9, 1), (9, 9, 1), (9, 10, 1), (9, 10, 0)], [(3, 2, 0), (3, 1, 0), (3, 1, 1), (3, 0, 1), (4, 0, 1), (5, 0, 1), (6, 0, 1), (7, 0, 1), (7, 0, 0), (8, 0, 0), (9, 0, 0), (9, 0, 1), (10, 0, 1), (11, 0, 1), (11, 1, 1), (12, 1, 1), (13, 1, 1), (13, 2, 1), (13, 2, 0), (14, 2, 0)], [(4, 5, 0), (4, 6, 0), (4, 6, 1), (4, 7, 1), (5, 7, 1), (5, 7, 2), (6, 7, 2), (7, 7, 2), (7, 6, 2), (8, 6, 2), (9, 6, 2), (10, 6, 2), (11, 6, 2), (11, 6, 1), (11, 7, 1), (11, 7, 0), (11, 8, 0)], [(9, 8, 0), (9, 7, 0), (10, 7, 0), (10, 6, 0), (11, 6, 0), (11, 5, 0)], [(1, 5, 0), (1, 5, 1), (1, 6, 1), (1, 6, 2), (1, 7, 2), (2, 7, 2), (3, 7, 2), (3, 8, 2), (4, 8, 2), (5, 8, 2), (6, 8, 2), (7, 8, 2), (8, 8, 2), (8, 7, 2), (9, 7, 2), (9, 7, 1), (9, 8, 1), (9, 8, 0)], [(6, 8, 0), (6, 9, 0), (6, 10, 0), (6, 11, 0), (7, 11, 0), (8, 11, 0), (9, 11, 0), (10, 11, 0), (11, 11, 0), (12, 11, 0)], [(13, 7, 0), (14, 7, 0), (14, 6, 0), (14, 5, 0), (14, 5, 1), (14, 5, 2), (14, 4, 2), (14, 4, 3), (13, 4, 3), (12, 4, 3), (11, 4, 3), (10, 4, 3), (9, 4, 3), (9, 3, 3), (9, 2, 3), (8, 2, 3), (7, 2, 3), (6, 2, 3), (5, 2, 3), (4, 2, 3), (4, 1, 3), (4, 0, 3), (3, 0, 3), (2, 0, 3), (1, 0, 3), (1, 0, 2), (1, 0, 1), (1, 0, 0), (1, 1, 0)], [(15, 1, 0), (15, 2, 0), (15, 3, 0), (15, 4, 0), (14, 4, 0), (13, 4, 0), (13, 5, 0), (12, 5, 0), (11, 5, 0)], [(1, 11, 0), (1, 11, 1), (1, 11, 2), (1, 11, 3), (1, 10, 3), (2, 10, 3), (3, 10, 3), (4, 10, 3), (5, 10, 3), (5, 9, 3), (5, 8, 3), (6, 8, 3), (7, 8, 3), (8, 8, 3), (9, 8, 3), (10, 8, 3), (11, 8, 3), (11, 7, 3), (12, 7, 3), (13, 7, 3), (13, 6, 3), (13, 5, 3), (12, 5, 3), (12, 5, 2), (12, 4, 2), (12, 3, 2), (12, 3, 1), (12, 3, 0)], [(16, 7, 0), (16, 7, 1), (16, 6, 1), (16, 5, 1), (16, 4, 1), (15, 4, 1), (14, 4, 1), (14, 3, 1), (14, 3, 2), (13, 3, 2), (13, 2, 2), (12, 2, 2), (12, 2, 1), (12, 2, 0)], [(2, 10, 0), (3, 10, 0), (3, 9, 0), (4, 9, 0), (5, 9, 0), (5, 9, 1), (6, 9, 1), (7, 9, 1), (7, 9, 0), (8, 9, 0), (9, 9, 0), (9, 8, 0)], [(11, 8, 0), (11, 9, 0), (10, 9, 0), (10, 10, 0), (9, 10, 0)], [(14, 2, 0), (14, 3, 0), (13, 3, 0), (13, 3, 1), (13, 4, 1), (13, 4, 2), (13, 5, 2), (13, 6, 2), (13, 7, 2), (13, 8, 2), (12, 8, 2), (12, 9, 2), (11, 9, 2), (10, 9, 2), (10, 10, 2), (9, 10, 2), (8, 10, 2), (7, 10, 2), (6, 10, 2), (5, 10, 2), (4, 10, 2), (3, 10, 2), (2, 10, 2), (1, 10, 2), (1, 10, 1), (1, 10, 0), (1, 9, 0)], [(1, 5, 0), (0, 5, 0), (0, 4, 0), (0, 4, 1), (0, 4, 2), (1, 4, 2), (1, 3, 2), (1, 2, 2), (1, 2, 3), (1, 2, 4), (2, 2, 4), (3, 2, 4), (4, 2, 4), (5, 2, 4), (5, 1, 4), (5, 1, 3), (6, 1, 3), (7, 1, 3), (8, 1, 3), (8, 1, 2), (9, 1, 2), (10, 1, 2), (11, 1, 2), (12, 1, 2), (13, 1, 2), (14, 1, 2), (15, 1, 2), (15, 1, 1), (15, 1, 0)], [(6, 8, 0), (5, 8, 0), (4, 8, 0), (4, 8, 1), (3, 8, 1), (3, 7, 1), (2, 7, 1), (1, 7, 1), (1, 8, 1), (1, 8, 0), (1, 9, 0)]]
for i in range(0):
## random.seed("piza")
skips = 0
netlist = Data.netlist_4
netlist = Grid.sortDistance(netlist)
connections_per_chip = netlist_checker.connectionsPerChip(netlist, chips)
path_grid = Grid.createPathGrid()
grid = Grid.createGrid()
neighbour_grid = createNeighbourGrid()
# assert False
relay_list = [0 for i in netlist]
relay_badness, max_path_length, max_itterations, max_random_moves, num_random_tries = 15, 60, 3000, 10, 3
shortest_paths = findPaths(netlist, relay_badness, max_path_length, max_itterations, max_random_moves, num_random_tries)
print shortest_paths
print relay_list
print skips
aantal_paden_gelegd = len([path for path in shortest_paths.values() if len(path) > 0])
totaal_paden = len(netlist)
# safe output
if aantal_paden_gelegd == totaal_paden:
Controle.safe(netlist, shortest_paths, relay_list)
layer = 0
Visualization.runVisualization(shortest_paths.values(), layer)
# Visualization.run3DVisualisation(shortest_paths.values(), "joris is cool")h
def show_all(self):
Visualization.plot_data_pointsXX(self.part.windows, xlim=None, ylim=None, filename=False, dims=None)
for node in queue:
if node[3] == successor[3] and successor[1] < node[1]:
queue.remove(node)
break
for successor in successors:
for node in closed_list:
if len(closed_list) != 0:
if node[3] == successor[3] and successor[1] < node[1]:
closed_list.remove(node)
break
for successor in successors:
heappush(queue, successor)
heappush(closed_list, current_point)
# print queue, end
if __name__ == "__main__":
netlist = data.sortDistance(netlist)
# netlist = [netlist[i] for i in range(40, 50)]
netlist = [netlist[40]]
paths = []
for net in netlist:
start_end = calculateEndStart(chips[net[0]], chips[net[1]])
path = Astar(start_end[0], start_end[1])
paths.append(path[0])
print path
Visualization.runVisualization(paths, 0)
def parse_one_file(input_data):
# looking for cached results
cache_filename = input_data.infile + '.cache'
## BRANCH: parsed infile already cached
if ( USE_PCAP_CACHE and os.path.isfile(cache_filename) ):
print "Reading cache:", cache_filename
pickle_input = open(cache_filename, 'rb')
senders = pickle.load(pickle_input)
pickle_input.close()
## BRANCH: no cache
else:
## * parse pcap file *
senders = Pcap_Parser.parse(input_data.infile, PACKETS) # 100000
## caching parser results
if ( USE_PCAP_CACHE ):
pickle_output = open(cache_filename, 'wb')
pickle.dump(senders, pickle_output, pickle.HIGHEST_PROTOCOL)
pickle_output.close()
##
# types = ( Storage_Classes.Sender.TYPE.AP, \
# Storage_Classes.Sender.TYPE.STATION, \
# Storage_Classes.Sender.TYPE.UNKNOWN)
types = ( Storage_Classes.Sender.TYPE.AP, )
# ## FIXME at the moment "s.show(addr)" is important for proper functionality
for t in types:
for addr in senders:
s = senders[addr]
if ( s.type == t ):
# s.show(addr)
s.set_addr(addr)
## Visualization
# Visualization.show_biggest_ap(senders)
## Units
sender = get_biggest_ap(senders)
# sender = get_biggest_ap(senders)
print
print "Using:"
sender.show()
# window sizes
# UNIT_WINDOW = 0.1
UNIT_WINDOW = 1.0
DATA_POINT_WINDOW = 6.0
# DATA_POINT_WINDOW = 5.0
# SKIP_FRONT = 20
SKIP_FRONT = 0
OVERLAPPING = True
## Data Grouping ##
units = Data_Grouping.build_units(sender, input_data.annotation, UNIT_WINDOW, SKIP_FRONT)
print "created units:", len(units), "(" + str(len(units) * units[0].length) + "s)"
parts = Data_Grouping.separation(units)
part = parts[0]
part.windows = Data_Grouping.windowing(part, DATA_POINT_WINDOW, OVERLAPPING)
part.features = Features.calculate_features(part)
# ## XXX
# for x in units:
# print x.show()
## XXX
# for x in part.features:
# if ( not x.invalid ):
# print "|||", x
print "new features:", len(part.features)
## plot into file
prepare_dir(input_data.group.plot_base_dir)
filename = input_data.group.plot_base_dir + "/" + os.path.splitext(os.path.basename(input_data.infile))[0] + ".pdf"
## XXX do pickles in the plot dir, too
if ( PICKLE_FEATURES ):
pick_path = input_data.group.plot_base_dir + "/" + os.path.splitext(os.path.basename(input_data.infile))[0] + "_features.pickle"
pickle_output = open(pick_path, 'wb')
pickle.dump(part, pickle_output, pickle.HIGHEST_PROTOCOL)
pickle_output.close()
## xlim = [units[0].start, 200]
# xlim = [20, 200]
# ylim = [-75, -15]
# print ">>>>>>> Plotting into:", filename
# Visualization.plot_mean_and_variance_into_file(units, xlim, ylim, filename)
# Visualization.plot_min_max_rssi(units, xlim, ylim, filename)
## plot data_points into file
# xlim = [0, 350]
# ylim = [-5, 10]
xlim = None
ylim = None
# Visualization.plot_data_points(data_points, xlim, ylim, filename)
# Visualization.plot_data_points(merged_points, xlim, ylim, filename, invalid_points = invalid_points)
Visualization.plot_data_points(part.features, xlim, ylim, filename)
# ylim = [0, 2]
# Visualization.plot_data_points(level_points, xlim, ylim, filename)
## XXX visualize raw rssi data (interactive)
## -- BE CAREFUL: this will not work in parallel processing mode
Visualization.plot_raw_rssi(sender)
print "-----------------------------------------------------------------------"
header = None
# header = \
#'''Activity\tmean\tvariance\tdistance\tdiff\tsign\tlevels
#discrete\tcontinuous\tcontinuous\tcontinuous\tcontinuous\tdiscrete\tcontinuous
#class\t\t\t\t\t
#'''
# orange_data = Orange_Export.Data_Collection(merged_points, header)
orange_data = Orange_Export.Data_Collection(part.features, None)
## return
# return units
return orange_data
netlist = Grid.sortDistance(netlist)
relay_list = [0 for i in netlist]
path_grid = Grid.createPathGrid()
grid = Grid.createGrid()
start_time = time.time()
comp = layIntersectingPaths()
intersecting_paths, paths_dict = comp[0], comp[1]
paths = simulatedAnnealing(intersecting_paths, paths_dict, max_iteration=1800)
end_time = time.time()
total_length = calculateWireLenght(paths.values())
print paths
print "Total wire length = ", total_length, "Computing time = ", end_time - start_time, " seconds or ", (end_time - start_time)/60, "minutes"
Visualization.runVisualization(paths.values(), 0)
Visualization.run3DVisualisation(paths.values(), 0)
smoothed_paths = []
for path in paths.values():
smoothed_paths.append(superSmoothPath(path))
total_length = calculateWireLenght(smoothed_paths)
print smoothed_paths
print "Total wire length = ", total_length, "Computing time = ", end_time - start_time, " seconds or ", (end_time - start_time)/60, "minutes"
Visualization.runVisualization(smoothed_paths, 0)
Visualization.run3DVisualisation(smoothed_paths, 0)
def showButton(self):
filename=self.getCurrentDataset()
dataset,attr=arff.parseArff(filename)
vis.visualizeLabels(dataset)
def simulate(ntrials, region, T, printonswap=False, showvis=True, newfig=False,
teamdesc=None, printbrackets=True):
"""
If region is "west" "midwest" "south" or "east" we'll run a bracket based
just on those teams.
If it's "all" we'll run a full bracket.
If it's a list of teams, we'll run a bracket based just on that list.
So, one way you might want to do things is to simulate 10000 runs for each
of the four brackets,
then run your final four explicitly, e.g.
T = 1.5
simulate(10000,'midwest',T)
# record results
simulate(10000,'south',T)
# record results
simulate(10000,'west',T)
# record results
simulate(10000,'east',T)
# record results
simulate(10000,['Louisville','Kansas','Wisconsin','Indiana'],T)
"""
if type(region) in (type([]), type(())):
teams = region[:]
else:
teams = RAS.teams[region]
b = Bracket(teams, T)
energy = b.energy()
ng = sum(b.games_in_rounds) # total number of games
# Let's collect some statistics
brackets = []
for trial in xrange(ntrials):
g = randint(0, ng) # choose a random game to swap
#print "attempted swap for game",g#,"in round",round[g]
#newbracket = deepcopy(b)
newbracket = b.copy()
newbracket.swap(g)
newenergy = newbracket.energy()
ediff = newenergy - energy
if ediff <= 0:
b = newbracket
energy = newenergy
if printonswap:
print "LOWER"
print b
else:
if random() < exp(-ediff/T):
b = newbracket
energy = newenergy
if printonswap:
print "HIGHER"
print b
brackets.append(b)
lb, mcb, mcb_count, unique_brackets, lowest_sightings = \
Stats.gather_uniquestats(brackets)
if showvis:
Visualization.showstats(brackets, unique_brackets, lowest_sightings,
newfig=newfig, teamdesc=teamdesc)
if printbrackets:
print "Lowest energy bracket"
print lb
print "Most common bracket (%s)"%mcb_count
print mcb
return (lb,mcb,mcb_count)
def cluster_map(request, data_set, classification1, classification2):
errors = []
warnings = []
form = None
valid = False
hasDataSet = False
clusterData = None
dataSetNames = []
selectedClassificationDisplay = ''
selectedClass = ''
minNodeSize = 99999
maxNodeSize = 0
minEdgeWeight = 99999
maxEdgeWeight = 0
minNodeSizeWithLabel = 20
maxNNodes = 20
topN = 10
previousNYears = 20
targetCPCColumnName = 'CPCs'
outFileName = 'clusterMapInput'
outFolderName = '../templates/visualization/'
fileType = '.json'
dataSetNames = []
datasets = Datasets.objects.all()
for dataset in datasets:
dataSetNames.append(dataset.name)
dataSetNames.insert(0, 'index')
classificationNames = dbq.getClassificationList()
classificationNames.insert(0, 'index')
# Model setup view
if (not (data_set == 'index' or classification1 == 'index'
or classification2 == 'index'
or classification1 == classification2)):
# df = dbq.getDataSetPatents(data_set)
# if(len(df.index)>1000):
# df = df.sample(n=500, replace=False, random_state=17)]
df = pd.DataFrame()
df = dbq.getDataSetPatentColumn(data_set, df, classification1)
selectedClass1 = df[classification1].tolist()
df = dbq.getDataSetPatentColumn(data_set, df, classification2)
selectedClass2 = df[classification2].tolist()
df = dbq.getDataSetPatentYears(data_set, df)
years = df['Years']
maxYear = max(years)
minYear = maxYear - previousNYears + 1
df = df[df.Years >= minYear]
allCategories = []
uniqueCategories1 = []
uniqueCategories2 = []
combinedCategories = []
allClass1 = []
allClass2 = []
for cList1 in selectedClass1:
if (cList1 == cList1 and cList1 != None):
for c in cList1:
if (c != 'nan' and c != '' and c != 'NAN' and c != 'Nan'):
allClass1.append(c)
for cList2 in selectedClass2:
if (cList2 == cList2 and cList2 != None):
for c in cList2:
if (c != 'nan' and c != '' and c != 'NAN' and c != 'Nan'):
allClass2.append(c)
expandedDF1 = pd.DataFrame()
expandedDF1[classification1] = allClass1
expandedDF2 = pd.DataFrame()
expandedDF2[classification2] = allClass2
grouped = expandedDF1.groupby([classification1
]).size().reset_index(name='nPPA')
topNClassification1 = grouped.nlargest(
topN, 'nPPA')[classification1].tolist()
grouped = expandedDF2.groupby([classification2
]).size().reset_index(name='nPPA')
topNClassification2 = grouped.nlargest(
topN, 'nPPA')[classification2].tolist()
# for c2, c3, c4 in zip(categories2, categories3, categories4):
for c1, c2 in zip(selectedClass1, selectedClass2):
if (not c1):
c1 = []
if (not c2):
c2 = []
c1 = [c for c in c1 if c in topNClassification1]
c2 = [c for c in c2 if c in topNClassification2]
allCategories = allCategories + c1 + c2
combinedCategories.append(c1 + c2)
uniqueCategories1 = uniqueCategories1 + c1
uniqueCategories2 = uniqueCategories2 + c2
uniqueCategories1 = list(set(uniqueCategories1))
uniqueCategories2 = list(set(uniqueCategories2))
# expanded = pd.DataFrame()
# expanded['Categories'] = allCategories
# categorySizes = expanded.groupby(['Categories']).size().reset_index(name='nPPA')
# categoryList = categorySizes['Categories'].tolist()
# categorySizesList = categorySizes['nPPA'].tolist()
selectedClass = combinedCategories
# selectedClass = categoryByKeywords
# wordList = []
# f = open('../out/words.txt', 'r')
# for line in f:
# wordList.append(line.rstrip())
# f.close()
# titleWords = pp.normalizeCorpus(df['Titles'].tolist(), wordList)
allClass = []
for c in selectedClass:
if (c):
allClass = allClass + list(filter(lambda a: a != '', c))
expanded = pd.DataFrame()
expanded['Class'] = allClass
classSizes = expanded.groupby(['Class'
]).size().reset_index(name='nPPA')
classList = classSizes['Class'].tolist()
classSizesList = classSizes['nPPA'].tolist()
grouped = expanded.groupby(
['Class']).size().reset_index(name='Number of P/PA')
topNClass = grouped.nlargest(10, 'Number of P/PA')['Class'].tolist()
# Cleaning of CPC
relationships = selectedClass
relationshipsEval = []
if (maxNNodes > 0):
topNNodes = v.getTopNNodes(relationships, maxNNodes)
for rList in relationships:
tempRList = []
for node in list(filter(lambda a: a != '', rList)):
if (node in topNNodes):
tempRList.append(node)
relationshipsEval.append(tempRList)
else:
for rList in relationships:
relationshipsEval.append(list(filter(lambda a: a != '',
rList)))
source = []
target = []
weight = []
for r in relationshipsEval:
pairs = combinations(r, 2)
for p in pairs:
if ((p[0] in uniqueCategories1 and p[1] in uniqueCategories1)
or
(p[0] in uniqueCategories2 and p[1] in uniqueCategories2)):
continue
else:
source.append(p[0])
target.append(p[1])
weight.append(1)
# source.append(p[0])
# target.append(p[1])
# weight.append(1)
newDF = pd.DataFrame()
newDF['source'] = source
newDF['target'] = target
newDF['weight'] = weight
graphDF = newDF.groupby(['source', 'target']).sum().reset_index()
maxEdgeWeight = graphDF['weight'].max()
minEdgeWeight = graphDF['weight'].min()
# graphDF.to_excel(outFolderName + 'edgelist.xlsx')
G = nx.from_pandas_edgelist(graphDF, 'source', 'target', 'weight')
G2 = nx.convert_node_labels_to_integers(G, label_attribute='name')
# Determine node groups using Louvain modularity
# communities = best_partition(G2, weight='size')
d = nx.readwrite.json_graph.node_link_data(G2, {'name': 'index'})
nodeNames = []
nodeCommunities = []
nodeSizes = []
nodeTop10 = []
for node in d['nodes']:
name = node['name']
# size = G2.degree[list(G.nodes()).index(node['name'])]
size = classSizesList[classList.index(node['name'])]
community = 2
if (name in uniqueCategories1):
community = 0
if (name in uniqueCategories2):
community = 1
# community = communities[list(G.nodes()).index(node['name'])]
node['size'] = size
node['group'] = community
nodeNames.append(name)
nodeSizes.append(size)
nodeCommunities.append(community)
name = node['name']
if (node['size'] < minNodeSize):
minNodeSize = node['size']
if (node['size'] > maxNodeSize):
maxNodeSize = node['size']
# minNodeSizeWithLabel = 0.2 * maxNodeSize
# for node in d['nodes']:
# if(node['size'] < minNodeSizeWithLabel):
# node['name'] = None
for node in d['nodes']:
if (not node['name'] in topNClass):
node['fontSize'] = 8
node['opacity'] = 0.5
else:
node['fontSize'] = node['size']
node['opacity'] = 1
nodesDF = pd.DataFrame()
nodesDF['CPC'] = nodeNames
nodesDF['Size'] = nodeSizes
nodesDF['Community'] = nodeCommunities
del d["directed"]
del d["multigraph"]
del d["graph"]
clusterData = d
hasDataSet = True
valid = True
templateHTML = 'visualization/cluster_map.html'
mainHTML = render_to_string(
templateHTML, {
'form': form,
'valid': valid,
'errors': errors,
'warnings': warnings,
'data_set': data_set,
'classification1': classification1,
'classification2': classification2,
'classificationNames': classificationNames,
'selectedClassificationDisplay': selectedClassificationDisplay,
'hasDataSet': hasDataSet,
'dataSetNames': dataSetNames,
'minNodeSize': minNodeSize,
'maxNodeSize': maxNodeSize,
'maxEdgeWeight': maxEdgeWeight,
'minEdgeWeight': minEdgeWeight,
'clusterData': clusterData,
'previousNYears': previousNYears,
})
return mainHTML
def view(self, first=0, last=None, step=1, object = None):
"""Show an animation of |object| using the positions in the
trajectory at all time steps from |first| to |last| with an
increment of |skip|. |object| defaults to the entire universe."""
Visualization.viewTrajectory(self, first, last, step, object)
def word_cluster_map(request, data_set, column):
errors = []
warnings = []
form = None
valid = False
hasDataSet = False
clusterData = None
dataSetNames = []
selectedClassificationDisplay = ''
minNodeSize = 99999
maxNodeSize = 0
minEdgeWeight = 99999
maxEdgeWeight = 0
minNodeSizeWithLabel = 20
maxNNodes = 30
previousNYears = 20
topN = 10
dataSetNames = []
datasets = Datasets.objects.all()
for dataset in datasets:
dataSetNames.append(dataset.name)
dataSetNames.insert(0, 'index')
columnNames = ['titles', 'abstracts', 'independent_claims']
columnNames.insert(0, 'index')
# Model setup view
if (not (data_set == 'index' or column == 'index')):
if (request.method == "POST"):
maxNNodes = int(request.POST.get('target-n-nodes'))
previousNYears = int(request.POST.get('target-n-years'))
# if(len(df.index)>1000):
# df = df.sample(n=500, replace=False, random_state=17)]
df = pd.DataFrame()
df = dbq.getDataSetPatentTACs(data_set, df)
df = dbq.getDataSetPatentYears(data_set, df)
years = df['Years']
maxYear = max(years)
minYear = maxYear - previousNYears + 1
df = df[df.Years >= minYear]
wordList = []
f = open('../out/words.txt', 'r')
for line in f:
wordList.append(line.rstrip())
f.close()
columnWords = []
if (column == 'titles'):
columnWords = pp.normalizeCorpus(df['Titles'].tolist(), wordList)
elif (column == 'abstracts'):
columnWords = pp.normalizeCorpus(df['Abstracts'].tolist(),
wordList)
elif (column == 'independent_claims'):
columnWords = pp.normalizeCorpus(df['Independent Claims'].tolist(),
wordList)
selectedColumn = columnWords
uniqueWords = []
combinedWords = []
allWords = []
for wordList in selectedColumn:
if (wordList == wordList and wordList != None):
for word in wordList:
if (word != 'nan' and word != '' and word != 'NAN'
and word != 'Nan'):
allWords.append(word)
expandedDF = pd.DataFrame()
expandedDF[column] = allWords
uniqueWords = list(set(allWords))
wordSizes = expandedDF.groupby([column
]).size().reset_index(name='nPPA')
topNWords = wordSizes.nlargest(topN, 'nPPA')[column].tolist()
wordList = wordSizes[column].tolist()
wordSizesList = wordSizes['nPPA'].tolist()
# Cleaning of CPC
relationships = selectedColumn
relationshipsEval = []
if (maxNNodes > 0):
topNNodes = v.getTopNNodes(relationships, maxNNodes)
for rList in relationships:
tempRList = []
for node in list(filter(lambda a: a != '', rList)):
if (node in topNNodes):
tempRList.append(node)
relationshipsEval.append(tempRList)
else:
for rList in relationships:
relationshipsEval.append(list(filter(lambda a: a != '',
rList)))
source = []
target = []
weight = []
for r in relationshipsEval:
pairs = combinations(r, 2)
for p in pairs:
source.append(p[0])
target.append(p[1])
weight.append(1)
newDF = pd.DataFrame()
newDF['source'] = source
newDF['target'] = target
newDF['weight'] = weight
graphDF = newDF.groupby(['source', 'target']).sum().reset_index()
maxEdgeWeight = graphDF['weight'].max()
minEdgeWeight = graphDF['weight'].min()
# graphDF.to_excel(outFolderName + 'edgelist.xlsx')
G = nx.from_pandas_edgelist(graphDF, 'source', 'target', 'weight')
G2 = nx.convert_node_labels_to_integers(G, label_attribute='name')
# Determine node groups using Louvain modularity
communities = best_partition(G2, weight='size')
d = nx.readwrite.json_graph.node_link_data(G2, {'name': 'index'})
nodeNames = []
nodeCommunities = []
nodeSizes = []
nodeTop10 = []
for node in d['nodes']:
name = node['name']
# size = G2.degree[list(G.nodes()).index(node['name'])]
size = wordSizesList[wordList.index(node['name'])]
community = communities[list(G.nodes()).index(node['name'])]
node['size'] = size
node['group'] = community
nodeNames.append(name)
nodeSizes.append(size)
nodeCommunities.append(community)
name = node['name']
if (node['size'] < minNodeSize):
minNodeSize = node['size']
if (node['size'] > maxNodeSize):
maxNodeSize = node['size']
# minNodeSizeWithLabel = 0.2 * maxNodeSize
# for node in d['nodes']:
# if(node['size'] < minNodeSizeWithLabel):
# node['name'] = None
for node in d['nodes']:
if (not node['name'] in topNWords):
node['fontSize'] = 8
node['opacity'] = 0.5
else:
node['fontSize'] = node['size']
node['opacity'] = 1
nodesDF = pd.DataFrame()
nodesDF['CPC'] = nodeNames
nodesDF['Size'] = nodeSizes
nodesDF['Community'] = nodeCommunities
del d["directed"]
del d["multigraph"]
del d["graph"]
clusterData = d
hasDataSet = True
valid = True
templateHTML = 'visualization/word_cluster_map.html'
mainHTML = render_to_string(
templateHTML, {
'form': form,
'valid': valid,
'errors': errors,
'warnings': warnings,
'data_set': data_set,
'column': column,
'columnNames': columnNames,
'hasDataSet': hasDataSet,
'dataSetNames': dataSetNames,
'minNodeSize': minNodeSize,
'maxNodeSize': maxNodeSize,
'maxEdgeWeight': maxEdgeWeight,
'minEdgeWeight': minEdgeWeight,
'clusterData': clusterData,
'maxNNodes': maxNNodes,
'previousNYears': previousNYears,
})
return mainHTML
with open('action_history_backup.pkl', 'wb') as output:
pickle.dump(action_history, output, pickle.HIGHEST_PROTOCOL)
with open('state_history_backup.pkl', 'wb') as output:
pickle.dump(state_history, output, pickle.HIGHEST_PROTOCOL)
with open('mean_error_history_backup.pkl', 'wb') as output:
pickle.dump(mean_error_history, output, pickle.HIGHEST_PROTOCOL)
expert.print()
# find out what are the ids that existed
region_ids = sorted(list(zip(*mean_error_history[-1]))[0])
Viz.plot_expert_tree(expert, region_ids)
#Viz.plot_evolution(state_history, title='State vs Time', y_label='S(t)', fig_num=1, subplot_num=261)
Viz.plot_evolution(action_history, title='Action vs Time', y_label='M(t)[1]', y_dim=1, fig_num=1, subplot_num=261)
Viz.plot_evolution(action_history, title='Action vs Time', y_label='M(t)[0]', y_dim=0, fig_num=1, subplot_num=262)
Viz.plot_model(expert, region_ids, x_idx=1, y_idx=0, fig_num=1, subplot_num=263)
Viz.plot_model(expert, region_ids, x_idx=2, y_idx=0, fig_num=1, subplot_num=269)
Viz.plot_regional_mean_errors(mean_error_history, region_ids, fig_num=1, subplot_num=234)
#Viz.plot_model_3D(expert, region_ids, x_idx=(0, 1), y_idx=0, fig_num=1, subplot_num=122)
Viz.plot_model_3D(expert, region_ids, x_idx=(1, 2), y_idx=0, fig_num=1, subplot_num=122, data_only=False)
plt.ioff()
plt.show()
def view(self, first=0, last=None, step=1, object = None): Visualization.viewTrajectory(self, first, last, step, object)
# netlist = [netlist[0], netlist[1], netlist[2], netlist[3], netlist[4], netlist[5]]
netlist = [netlist[i] for i in range(35)]
# netlist = [netlist[6]]
netlist = [netlist[i] for i in range(11)]
for net in netlist:
path = []
start, end = chips[net[0]], chips[net[1]]
print "finding a path betweeen: ", chips[net[0]], chips[net[1]]
original_value_start, original_value_end = isFree(start), isFree(end)
while len(path) < 1:
try:
path, grid = findPossiblePath(start, end, grid)
break
except PathLengthError:
break
setOccupation(start, original_value_start)
setOccupation(end, original_value_end)
print "Occupation is changed"
print 'PathLengthError'
shortest_paths.append(path)
print "The number of complete paths should be %i, the actual number of complete paths is %i " % (len(netlist), len(shortest_paths))
# print "The total wire length is %i and there are %i intersections of which there are %i on the chips" % (
# calculateWireLenght(shortest_paths),
# checkIntersections(shortest_paths), doubleStartEndPoints(netlist))
print shortest_paths
layer = 3
Visualization.runVisualization(shortest_paths, layer)
