def __init__(self,
gameSlide,
gameHotspot,
takenfile,
menuSlide,
closeupSlide=None,
id=None,
taken=False,
onTake=lambda item: None,
onUse=lambda item: None):
if id: Item.rows[id] = self
self.menuSlide = menuSlide
if menuSlide:
self.menuHotspot = Hotspot(self.menuSlide,
None,
onClick=self.use,
cursor='grab.png',
rectRel=RelativeRect((0, 0, 1, 1)))
self.menuSlide.add(self.menuHotspot)
self.closeupSlide = closeupSlide
if self.closeupSlide:
self.closeupPanel = Panel()
self.closeupPanel._layer = 11
self.closeupPanel.rect = pyzzle.screen.get_rect()
self.closeupHotspot = Hotspot(self.closeupSlide,
None,
onClick=self.exit,
cursor='fwd.png',
layer=-1)
self.closeupHotspot.rect = pyzzle.screen.get_rect()
self.closeupSlide.parent = self.closeupPanel
self.closeupSlide._getRect()
self.gameSlide = gameSlide
if type(gameHotspot) == Hotspot:
self.gameHotspot = gameHotspot
else:
self.gameHotspot = Hotspot(self.gameSlide,
None,
rectRel=gameHotspot)
self.gameHotspot.cursor = 'grab.png'
self.gameHotspot.onClick = self.take
self.gameHotspot.parent = self.gameSlide
self.takenfile = takenfile
self.taken = taken
if taken and self.menuSlide:
self.inventory.add(self.menuSlide)
elif gameSlide:
gameSlide.add(self.gameHotspot)
self.onUse = onUse
self.onTake = onTake
def __hotspot_variants(self, logger):
logger.info("Beginning variant hotspotting...")
hotspotter = Hotspot(self.project_config, self.mongodb, logger)
hotspotter.hotspot_variants(self.args['cpu_number'])
self.mongodb.open_connection()
self.project_config = self.mongodb.get_project_config(self.args['project_name'])
self.mongodb.close_connection()
logger.info("Variant hotspotting successfully completed")
def hotspot(self):
hotspot = Hotspot()
if "new" == self.args['number']:
hotspot.run()
else:
try:
number = int(self.args['number'])
hotspot.run(number)
except ValueError:
self.logger.error("The number you specified is not a proper integer number")
sys.exit()
def main():
# method to check if exit was entered anywhere, exit the program with 0 as the exit status
def check_exit(input_to_check):
if input_to_check == "exit":
sys.exit(0)
print('Welcome to WiFiFi a small windows hotspot application, Type exit to close the program at anytime')
# ask for existing profile and create a new one if none exists
while True:
yes = input('Do you have an existing profile?, Enter Yes to proceed or No to create a new one\n')
yes.lower()
check_exit(yes)
if yes == "yes":
hotspot = Hotspot()
hotspot.start()
break
# capture the username and password from the user
elif yes == "no":
name = input("Enter the Name of the New network:\n")
password = ""
check_exit(name)
while len(password) < 8:
password = input("""Enter the password for the network
hint: password must be at least eight characters: """)
hotspot = Hotspot(name, password)
hotspot.initialize_hotspot()
hotspot.start()
break
else:
print("Invalid option please enter Yes or No:\n")
continue
# prompt the user to end the active hotspot session
while True:
stop = input("type stop to stop the wireless network:\n")
stop.lower()
if stop == "stop":
hotspot.stop()
# should modify the check_exit function to accept an optional argument instead of using sys
sys.exit(0)
else:
print('invalid option type stop to stop the wireless network:\n')
continue
def test_filter_genes():
"""
Ensure genes with no expression are pre-filtered
"""
# Simulate some data
N_CELLS = 100
N_DIM = 10
N_GENES = 10
N_GENES_ZERO = 5
latent = sim_data.sim_latent(N_CELLS, N_DIM)
latent = pd.DataFrame(latent)
umi_counts = sim_data.sim_umi_counts(N_CELLS, 2000, 200)
umi_counts = pd.Series(umi_counts)
gene_exp = np.random.rand(N_GENES + N_GENES_ZERO, N_CELLS)
gene_exp[N_GENES:] = 0
gene_exp = pd.DataFrame(
gene_exp,
index=['Gene{}'.format(i + 1) for i in range(gene_exp.shape[0])],
columns=latent.index)
hs = Hotspot(gene_exp,
model='normal',
latent=latent,
umi_counts=umi_counts)
assert hs.counts.shape[0] == N_GENES
def hotspotDirective(_context, name, obj=None, interface=None,
resource=[], considerparams=[]):
if not obj and not interface and not resource:
raise ConfigurationError(u"Du solltest dich entscheiden, Jonny!")
hotspot = Hotspot(obj, interface, resource, considerparams)
utility(_context,
provides=IHotspot,
component=hotspot,
name=name)
def hotspot(self):
"""
This carries out the hotspotting option.
:return:
"""
hotspot = Hotspot()
# If "new" is specified as the hotspot option.
if "new" == self.args['number']:
hotspot.run()
else:
try:
# Make sure that the number given is an actual number.
number = int(self.args['number'])
hotspot.run(number)
except ValueError:
self.logger.error("The number you specified is not a proper integer number")
sys.exit()
def test_models():
"""
Ensure each model runs
"""
# Simulate some data
N_CELLS = 100
N_DIM = 10
N_GENES = 10
latent = sim_data.sim_latent(N_CELLS, N_DIM)
latent = pd.DataFrame(
latent, index=['Cell{}'.format(i + 1) for i in range(N_CELLS)])
umi_counts = sim_data.sim_umi_counts(N_CELLS, 2000, 200)
umi_counts = pd.Series(umi_counts)
gene_exp = np.random.rand(N_GENES, N_CELLS)
gene_exp = pd.DataFrame(
gene_exp,
index=['Gene{}'.format(i + 1) for i in range(gene_exp.shape[0])],
columns=latent.index)
for model in ['danb', 'bernoulli', 'normal', 'none']:
hs = Hotspot(gene_exp,
model=model,
latent=latent,
umi_counts=umi_counts)
hs.create_knn_graph(False, n_neighbors=30)
hs.compute_hotspot()
assert isinstance(hs.results, pd.DataFrame)
assert hs.results.shape[0] == N_GENES
hs.compute_autocorrelations()
assert isinstance(hs.results, pd.DataFrame)
assert hs.results.shape[0] == N_GENES
hs.compute_local_correlations(gene_exp.index)
assert isinstance(hs.local_correlation_z, pd.DataFrame)
assert hs.local_correlation_z.shape[0] == N_GENES
assert hs.local_correlation_z.shape[1] == N_GENES
hs.create_modules(min_gene_threshold=2, fdr_threshold=1)
assert isinstance(hs.modules, pd.Series)
assert (hs.modules.index & gene_exp.index).size == N_GENES
assert isinstance(hs.linkage, np.ndarray)
assert hs.linkage.shape == (N_GENES - 1, 4)
hs.calculate_module_scores()
assert isinstance(hs.module_scores, pd.DataFrame)
assert (hs.module_scores.index == gene_exp.columns).all()
threading.Thread(target=self.monitor_log,
args=(stop_flag, )).start()
# Monitors the log file and upates the text field when new data arrives
def monitor_log(self, stop_flag):
log_file = os.path.join(self.root.base_dir, self.root.log_file)
with open(log_file) as log:
while not stop_flag.is_set():
line = log.readline()
if line:
self.text.insert('end', line)
self.text.see('end')
if __name__ == "__main__":
# Turns off autorepeat behaviour of os (enables detecting keyRelease and keyPress)
os.system('xset r off')
# Turn on hotspot
Hotspot.open_hotspot()
# Open the GUI and let it run until closed
gui = Gui()
gui.mainloop()
# Close hotspot before exiting
#Hotspot.close_hotspot()
# Turn aurorepeat back on before exiting
os.system('xset r on')
def hotspot():
"""
Hotspot route
"""
if request.method == "POST":
valid_form = functions.validate_form(request.form)
# Display error if any field is empty
if not valid_form["valid"]:
return render_template("index.html",
error=valid_form["error"],
data_chosen=valid_form["datachosen"],
setup=setup)
else:
# Setup the hotspot
# hotspot = functions.setup_hotspot(request.form, units)
hotspot = Hotspot(request.form, units)
if hotspot.datafile.endswith(".csv"):
datafile_as_dict = parse.csv_to_dict(hotspot.filter_value,
hotspot.filter_column,
hotspot.datafile)
hotspot.getis, hotspot.conf_levels = functions.calculate_hotspot(
hotspot, datafile_as_dict, "getis")
hotspot.data = functions.calculate_hotspot(
hotspot, datafile_as_dict)
elif hotspot.datafile.endswith(".log"):
hotspot.data, hotspot.getis, hotspot.conf_levels = functions.calculate_hotspot(
hotspot)
if hotspot.save_me:
print("Saving aoristic csv...")
functions.save_csv(hotspot.data, "static/maps/", hotspot.title,
"_aoristic.csv")
print("Saving getis csv...")
functions.save_csv(hotspot.getis, "static/maps/",
hotspot.title, "_gi.csv")
# Creates the getis hotspot
getis_hotspot = functions.create_hotspot(hotspot, "getis",
hotspot.pvalue)
# Save getis hotspot as png
functions.save_figure(getis_hotspot, "static/maps/", hotspot.title,
"_gi.png")
# Creates the aoristic hotspot
aoristic_hotspot = functions.create_hotspot(hotspot, "data")
# Save aoristic hotspot as png
functions.save_figure(aoristic_hotspot, "static/maps/",
hotspot.title, "_aoristic.png")
# Save the html table of confidence levels
functions.save_table(hotspot.title, hotspot.conf_levels)
# Get the saved pngs
filelist = functions.get_saved_png(hotspot.title)
#os.listdir('static/maps/' + hotspot["title"])
return render_template("hotspot.html",
folder=hotspot.title,
hotspots=filelist,
lisa=hotspot.conf_levels)
