def func11(file_name, mid):
if imghdr.what(file_name) in [None, 'gif']:
path = eu('~/www/media/storage/movie/') + f'{mid}.jpg'
subprocess.run(
['ffmpeg', ] + \
'-ss 7 -t 1 -r 1'.split(' ') + \
['-i', file_name] + \
f'-f image2 -s 320x240'.split(' ') +\
[path]
)
path = eu('~/www/media/storage/movie/')
cmd = ["ffmpeg", "-i", file_name] + \
'-map 0 -f segment -vcodec libx264 -acodec aac -strict experimental'.split(' ') + \
'-vf scale=640:-1 -vb 512k'.split(' ') + \
["-segment_list", f'{path}ts/{mid}.m3u8', '-segment_time', '2', f'{path}ts/{mid}-%03d.ts']
subprocess.run(cmd)
else:
path = eu('~/www/media/storage/movie/') + f'{mid}.jpg'
subprocess.run(
['ffmpeg', ] + \
'-ss 7 -t 1 -r 1'.split(' ') + \
['-i', file_name] + \
f'-f image2 -s 3200x2400'.split(' ') +\
[path]
)
os.remove(file_name)
def createproject(name):
if not exists(dataroot):
os.mkdir(dataroot)
if exists(dataroot + f"Project_{name}"):
print(f"Project {name} already exits!")
return 1
os.mkdir(eu(f"{dataroot}Project_{name}"))
os.mkdir(eu(f"{progroot}{name}"))
py = f'from os.path import expanduser as _eu\nprojectroot = _eu("{dataroot}Project_{name}")\n'
with open(f"{progroot}{name}/__init__.py", "w") as handle:
handle.write(py)
print(f"Created SciProject: {name}")
def main():
# Pull in the plugins
if call('git submodule update --init', shell=True) != 0:
if 'y' != input('Error during submodule (=plugin) init or update. Continue setup? [y*/n] '):
return 1
global backup
backup = raw_input('Delete existing files? [y/n]: ') != 'y'
here_to_home('bash')
bashrc = eu('~/.bashrc')
bashappend = open('_bashrc.append').read()
try:
if bashappend not in open(bashrc).read():
with open(bashrc, 'a') as f:
f.write(bashappend)
except IOError:
# Assume non-existing file. Create one.
# (Or no permission, this wont change anything in that case.)
with open(bashrc, 'w+') as f:
f.write(bashappend)
here_to_home('vimrc')
here_to_home('vim')
here_to_home('inputrc')
def updateproj(name):
try:
os.chdir(eu(f"~/SciProjects/{name}"))
except FileNotFoundError:
print("No such project:", name)
if input("Should I create it? y/N >") == "y":
return createproject(name)
return
subprocess.run(["git", "pull"])
def calculateOR(n11, n10, n01, n00):
ORnum = n11*n00
ORden = n01*n10
if ORnum == ORden == 0:
OR_uMLE, wald_MLE_CI95L, wald_MLE_CI95R = 'NaN', '', ''
wald_MLE_CI90L, wald_MLE_CI90R = '', ''
elif ORnum == 0:
OR_uMLE, wald_MLE_CI95L, wald_MLE_CI95R = 0, '', ''
wald_MLE_CI90L, wald_MLE_CI90R = '', ''
elif ORden == 0:
OR_uMLE, wald_MLE_CI95L, wald_MLE_CI95R = 'InF', '', ''
wald_MLE_CI90L, wald_MLE_CI90R = '', ''
else:
OR_uMLE = ORnum/ORden
# Wald test\tCI
lnOR = numpy.log(OR_uMLE)
SE_lnOR = numpy.sqrt(sum(map(lambda _:1/_ ,[n11,n10,n01,n00])))
wald_MLE_CI95L, wald_MLE_CI95R = numpy.exp(lnOR - 1.96*SE_lnOR), numpy.exp(lnOR + 1.96*SE_lnOR)
wald_MLE_CI90L, wald_MLE_CI90R = numpy.exp(lnOR - 1.645*SE_lnOR), numpy.exp(lnOR + 1.645*SE_lnOR)
if n11 + n10 + n01 + n00 >= 1000:
# G-test
cmd = ['Rscript', eu("~/Dropbox/age_final_submission/ageflu/scripts/ageflu_gtest.R")] + map(str,[n11, n10, n01, n00])
Routput = subprocess.check_output(cmd, universal_newlines=True, stderr=subprocess.PIPE).split('\n')
pval = float(Routput[1])
# small sample size CI - NaN
ss_CI90L, ss_CI90R, ss_CI95L, ss_CI95R = 'NaN', 'NaN', 'NaN', 'NaN'
else:
# Barnard's
cmd = ['Rscript', eu("~/Dropbox/age_final_submission/ageflu/scripts/ageflu_barnard.R")] + map(str,[n11, n10, n01, n00])
Routput = subprocess.check_output(cmd, universal_newlines=True, stderr=subprocess.PIPE).split('\n')
pval = float(Routput[-2].replace('[1]','').split()[1])
# Agresti\tMin unconditional exact CI for small sample sizes
cmd = ['Rscript', eu("~/Dropbox/age_final_submission/ageflu/scripts/agresti_and_min.R")] + map(str,[n11, n10, n01, n00, 0.9])
Routput = filter(None, subprocess.check_output(cmd, universal_newlines=True, stderr=subprocess.PIPE).split('\n'))
ss_CI90L, ss_CI90R = map(lambda _: _ if _ == 'Inf' else float(_), re.findall('(\d+\.\d+|\d+|Inf)', Routput[-1]))
cmd = ['Rscript', eu("~/Dropbox/age_final_submission/ageflu/scripts/agresti_and_min.R")] + map(str,[n11, n10, n01, n00, 0.95])
Routput = filter(None, subprocess.check_output(cmd, universal_newlines=True, stderr=subprocess.PIPE).split('\n'))
ss_CI95L, ss_CI95R = map(lambda _: _ if _ == 'Inf' else float(_), re.findall('(\d+\.\d+|\d+|Inf)', Routput[-1]))
return OR_uMLE, wald_MLE_CI90L, wald_MLE_CI90R, wald_MLE_CI95L, wald_MLE_CI95R, pval, ss_CI90L, ss_CI90R, ss_CI95L, ss_CI95R
def __init__(self):
try:
with open(eu("~/.config/waybackweather/darksky.json"), "r", encoding="utf8") as conf_json:
conf = json.load(conf_json)
self.API_KEY = conf["key"]
except Exception as e:
raise e
self.session = requests.Session()
self.session.headers.update({"User-Agent": f"WaybackWeather/{darksky.__version__}"})
def link_with_backup(source, link_name):
full_link_name = eu(link_name)
print('Installing ' + source + ' -> ' + full_link_name)
try:
os.symlink(source, full_link_name)
except OSError:
if backup:
os.rename(full_link_name, full_link_name + '.' + str(int(time())) + '.dotfiles_backup')
else:
os.remove(full_link_name)
os.symlink(source, full_link_name)
def get_number_of_monitors() -> int:
"""It gets the number of monitors.
Returns
-------
int
The number of active non-mirrored monitors.
"""
try:
output = subprocess.check_output(
eu("~/.config/qtile/check_number_of_monitors.sh"),
shell=True).decode()[:-1]
except subprocess.SubprocessError:
return 0
return int(output)
def link_with_backup(source, link_name, symbolic=True):
full_link_name = eu(link_name)
print('Installing ' + source + ' -> ' + full_link_name)
makedirs(dirname(full_link_name))
try:
if symbolic:
os.symlink(source, full_link_name)
else:
os.link(source, full_link_name)
except OSError:
if backup:
os.rename(full_link_name, full_link_name + '.' + str(int(time())) + '.dotfiles_backup')
else:
# Try to remove this thing. Non-empty directories don't work yet.
try:
os.remove(full_link_name)
except OSError as e:
os.rmdir(full_link_name)
os.symlink(source, full_link_name)
def widget_layout(self) -> list[_Widget]:
"""Module for showing layout and number of windows.
Returns
-------
list[libqtile.widget.base._Widget]
The list of widgets to add to the bar.
"""
# Widget for layout
widget_layout = CurrentLayoutIcon(
custom_icon_paths=[eu("~/.config/qtile/icons")],
scale=0.5,
padding=-5,
foreground=self.colors["green"],
)
# Widget for number of windows
widget_nw = WindowCount(**self.fonts["Normal"],
foreground=self.colors["green"],
show_zero=True)
widgets = [widget_layout, widget_nw]
return widgets
def btn4push(self, event):
for file in self.text_entry.GetValue().split('\n'):
shutil.move(file, eu('~/Downloads/変換済/'))
self.text2.SetValue(self.text2.GetValue() +
'%s : 移動しました' % datetime.now())
def btn2push(self, event):
ls = glob.glob(eu('~/Downloads/**/*.mp4'), recursive=True)
self.text_entry.SetValue('\n'.join(ls))
#! encoding: utf8
from unittest import TestCase, main
from proto.ils import qrmcp, reduction, search, ils
from numpy.random import rand, randint
from numpy import array, dot
from numpy.testing import assert_allclose, assert_array_equal
from oct2py import octave, Oct2Py
from os.path import expanduser as eu
octave.addpath(eu('~')+'/code/pylgrim/ils')
oc = Oct2Py()
m, n = 5, 3
print "Initital size of matrix B: %d × %d" % (m, n)
# B = rand(m, n)
B = array([[-1.38483, 0.53704, 0.14925], # ans:
[1.05734, 0.61432, 0.94116], # v1 v2
[-0.33438, -0.13293, -0.60755], # 1 1
[0.26814, 0.41059, -0.52649], # -2 -1
[-0.66335, -1.42715, -0.97412]]) # 3 2
z_true = array([1, -2, 3]).reshape(3, 1) # column vector
class TestQrmcp(TestCase):
def test_qrmcp(self):
y = dot(B, z_true) + 1e-3 * rand(m, 1)
R_qrmcp, piv, y = qrmcp(B, y)
R_true = [[-1.58217452, -1.20917892, -0.94591479],
[0, 1.19444506, -0.11444606],
print("------------------------")
print()
print("Done!")
print()
print("Successfully converted %d out of %d files!" % (len(all_midi_matrices), num_files))
print()
print("Saving array as .npy file...")
print()
np.save('midimatrices.npy', np.array(all_midi_matrices))
print("All done!")
if converting_errors:
print("Here are the ones that didn't convert: ")
for i, f in converting_errors:
print(f"{i}: {f}")
with open('converting_errors.txt', 'w') as fh:
fh.write("%s\n" % f)
if parsing_errors:
print("Here are the files that couldn't be parsed: ")
for i, f in parsing_errors:
print(f"{i}: {f}")
with open('parsing_errors.txt', 'w') as fh:
fh.write("%s\n" % f)
if __name__ == '__main__':
MidiMatrix(join(eu('~'), 'VGmidi/Balloon_Fight_-_Main_Theme_%28Dancing_Balloon%21_remix%29.mid')).mid_to_matrix()
'''Reads in addresses from DB stored at path, or backup,
to label phone numbers.'''
from helpers.utils import filter_based_on_col
from os.path import expanduser as eu
import os
import pandas as pd
import numpy as np
import sqlite3
import sys
COMP_PATH = eu(
"~/Library/Application Support/AddressBook/AddressBook-v22.abcddb")
ENDING = "AddressBook-v22.abcddb"
SRCS = eu("~/Library/Application Support/AddressBook/Sources")
MO_PTH = '31bb7ba8914766d4ba40d6dfb6113c8b614be442'
MO_BASE = eu('~/Library/Application Support/MobileSync/Backup/')
def extract_contacts(path):
'''Get Contact Data from PHONENUMBER, RECORD Tables. As in icloud_query.py'''
try:
ad_db = sqlite3.connect(path)
jn = pd.read_sql(
"""SELECT ZFULLNUMBER, ZSORTINGFIRSTNAME FROM ZABCDPHONENUMBER
LEFT OUTER JOIN ZABCDRECORD
ON ZABCDPHONENUMBER.ZOWNER = ZABCDRECORD.Z_PK""", ad_db)
clean = lambda x: filter(lambda y: '0' <= y <= '9', x)[-10:]
jn['ZFULLNUMBER'] = jn.ZFULLNUMBER.apply(clean)
cstart = zip(jn.ZFULLNUMBER, jn.ZSORTINGFIRSTNAME)
clist = {x[0]: x[1][:len(x[1]) / 2] for x in cstart}
return clist
from multiprocessing import Lock
from multiprocessing import Queue
import cma
from gammatone import gammatone
from dnn_protos import writeDoubleMatrix
from color_log import add_coloring_to_emit_ansi
POP_SIZE = 50
SIGMA = 2
BOUNDS = (0, 10)
CMA_JOBS = 4
VERBOSE = True
RUNS_DIR = eu("~/dnn/runs/mpl")
MPL_BIN = eu("~/dnn/bin/mpl")
MPL_CONF_JSON = eu("~/dnn/mpl.json")
MPL_TEST_DATA = eu("~/dnn/ts/riken_14chan_3LRR.pb")
MPL_DIM = 0
cma_conf = {
"log_freq": { "def" : True }, # non learn
"a" : { "def" : 10.0, }, # non learn
"b" : { "def" : 0.1, "min" : 0.1, "max" : 10},
"n": { "def" : 6, "min" : 0.1, "max" : 10},
"fnum": { "def" : 24}, #"min" : 12, "max" : 24},
"lb": { "def" : 0.0, "min" : 0, "max" : 5},
"hb": { "def" : 50.0, "min" : 10, "max" : 300},
"L": { "def" : 100.0}, # "min" : 10, "max" : 100},
"Tmax": { "def" : 1.0, "min" : 0.1, "max" : 10},
from multiprocessing import Lock
from multiprocessing import Queue
import cma
from gammatone import gammatone
from dnn_protos import writeDoubleMatrix
from color_log import add_coloring_to_emit_ansi
POP_SIZE = 50
SIGMA = 2
BOUNDS = (0, 10)
CMA_JOBS = 4
VERBOSE = True
RUNS_DIR = eu("~/dnn/mpl/cma_runs")
MPL_BIN = eu("~/cpp/build/bin/mpl")
MPL_CONF_JSON = eu("~/cpp/mpl.json")
MPL_TEST_DATA = eu("~/dnn/ts/riken_14chan_3LRR.pb")
MPL_DIM = 0
cma_conf = {
"log_freq": { "def" : True }, # non learn
"a" : { "def" : 10.0, }, # non learn
"b" : { "def" : 0.1, "min" : 0.1, "max" : 10},
"n": { "def" : 6, "min" : 0.1, "max" : 10},
"fnum": { "def" : 24}, #"min" : 12, "max" : 24},
"lb": { "def" : 0.0, "min" : 0, "max" : 5},
"hb": { "def" : 50.0, "min" : 10, "max" : 300},
"L": { "def" : 100.0}, # "min" : 10, "max" : 100},
"Tmax": { "def" : 1.0, "min" : 0.1, "max" : 10},
#! encoding: utf8
from unittest import TestCase, main
from proto.ils import qrmcp, reduction, search, ils
from numpy.random import rand, randint
from numpy import array, dot
from numpy.testing import assert_allclose, assert_array_equal
from oct2py import octave, Oct2Py
from os.path import expanduser as eu
octave.addpath(eu('~') + '/code/pylgrim/ils')
oc = Oct2Py()
m, n = 5, 3
print "Initital size of matrix B: %d × %d" % (m, n)
# B = rand(m, n)
B = array([
[-1.38483, 0.53704, 0.14925], # ans:
[1.05734, 0.61432, 0.94116], # v1 v2
[-0.33438, -0.13293, -0.60755], # 1 1
[0.26814, 0.41059, -0.52649], # -2 -1
[-0.66335, -1.42715, -0.97412]
]) # 3 2
z_true = array([1, -2, 3]).reshape(3, 1) # column vector
class TestQrmcp(TestCase):
def test_qrmcp(self):
y = dot(B, z_true) + 1e-3 * rand(m, 1)
R_qrmcp, piv, y = qrmcp(B, y)
R_true = [[-1.58217452, -1.20917892, -0.94591479],
from os.path import expanduser as eu
from hac import GreedyAgglomerativeClusterer
import networkx as nx
from collections import defaultdict
from itertools import combinations
# # Clustering!
# In this notebook, we perform the actual clustering. Given an input scenario, we:
# 1. perform all possible clusterings, from 1 to $\min\{|\mathcal{V},|,|\mathcal{H}|\}$;
# 2. for each possible clustering, check if a _straightforward_ clustering, where bigger VNF clusters are associated with bigger host clusters, is _prima facie_ feasible.
#
# The path of input and output files (both in JSON) are specified as environment variables.
# In[7]:
input_path = os.getenv('INPUT_PATH', eu('test/release2/test_req_sap_cp.json'))
output_path = os.getenv(
'OUTPUT_PATH', eu('test/release2/test_req_sap_cp_cluster_decisions.json'))
# Before creating a VNF graph, we treat those **SAPs associated to a VL** as a VNF with zero requirements
# In[15]:
def cluster(PARequest):
"""Executes the clustering of the PARequest
:PARequest: REST API PARequest
:returns: PARequest dictionary with the clustering decisions
"""
import os, time, sys
from win10toast import ToastNotifier
from infi.systray import SysTrayIcon
from os.path import expanduser as eu
def resource_path(relative_path):
"""is used for pyinstaller so it can read the relative path"""
if hasattr(sys, '_MEIPASS'):
return os.path.join(sys._MEIPASS, relative_path)
return os.path.join(os.path.abspath('.'), relative_path)
#resources
ico = resource_path("./gui/logo.ico")
toaster = ToastNotifier()
home = eu("~")
t = time.localtime()
current_time = time.strftime("%Y%m%d_%H%M%S", t)
try:
os.mkdir(eu("~"+"\\pictures\\screenshot\\"))
home = eu("~"+"\\pictures\\screenshot\\")
except FileExistsError:
home = eu("~"+"\\pictures\\screenshot\\")
def notification(message):
"""Windows10 notification"""
toaster.show_toast("Printscreen",
message,
icon_path=ico,
"e",
[
Key([], "l", lazy.shutdown(), desc="Log off"),
Key([], "r", lazy.spawn("systemctl reboot"), desc="Reboot PC"),
Key([], "p", lazy.spawn("systemctl poweroff"), desc="Shutdown"),
],
mode="exit: [l]ogout, [r]eboot, [p]oweroff",
),
# Search for app. Customized to use dracula theme.
# Tested with dmenu 5.0
Key([mod], "d", lazy.spawn("dmenu_run"), desc="Spawn dmenu"),
# Select monitor layout
Key(
[mod, "shift"],
"a",
lazy.spawn(eu("~/.bin/select-monitor.sh")),
desc="Select monitor layout using script",
),
]
# ============ Media Controls ============
playerctl = "playerctl -p spotify,%any"
keys += [
# Volume control
# Tested with pamixer 1.4.5
Key([],
"XF86AudioRaiseVolume",
lazy.spawn("pamixer -i 5"),
desc="Increase volume"),
Key([],
"XF86AudioLowerVolume",
'''Reads in addresses from DB stored at path, or backup,
to label phone numbers.'''
from helpers.utils import filter_based_on_col
from os.path import expanduser as eu
import os
import pandas as pd
import numpy as np
import sqlite3
import sys
COMP_PATH = eu("~/Library/Application Support/AddressBook/AddressBook-v22.abcddb")
ENDING = "AddressBook-v22.abcddb"
SRCS = eu("~/Library/Application Support/AddressBook/Sources")
MO_PTH = '31bb7ba8914766d4ba40d6dfb6113c8b614be442'
MO_BASE = eu('~/Library/Application Support/MobileSync/Backup/')
def extract_contacts(path):
'''Get Contact Data from PHONENUMBER, RECORD Tables. As in icloud_query.py'''
try:
ad_db = sqlite3.connect(path)
jn = pd.read_sql("""SELECT ZFULLNUMBER, ZSORTINGFIRSTNAME FROM ZABCDPHONENUMBER
LEFT OUTER JOIN ZABCDRECORD
ON ZABCDPHONENUMBER.ZOWNER = ZABCDRECORD.Z_PK""", ad_db)
clean = lambda x: filter(lambda y: '0' <= y <= '9', x)[-10:]
jn['ZFULLNUMBER'] = jn.ZFULLNUMBER.apply(clean)
cstart = zip(jn.ZFULLNUMBER, jn.ZSORTINGFIRSTNAME)
clist = {x[0]: x[1][:len(x[1])/2] for x in cstart}
return clist
except pd.io.sql.DatabaseError as e:
print "Non-fatal DB error ON path: ", path
return {}
#!/usr/bin/env python
import os
from os.path import expanduser as eu
os.system('rm ' + eu('~/.config/i3/blur.png'))
pic = eu('~/.config/i3/toBlur.png')
os.system('scrot {0}'.format(pic))
os.system('convert {0} -filter Gaussian -blur -2x10 '.format(pic) +
eu('~/.config/i3/blur.png'))
os.system('rm -f {0}'.format(pic))
os.system('i3lock -e -f -i ' + eu('~/.config/i3/blur.png'))
def main():
# Pull in the plugins
if call(['git', 'submodule', 'update', '--init']) != 0:
if input('Error during submodule (=plugin) init or update. Continue setup? [Y/n] ') not in ('y', 'Y', ''):
return 1
# Pull in Vundle (for vim, should make it a submodule at some point?)
if not exists(here('_vim/bundle/vundle')):
if call(['git', 'clone', 'https://github.com/gmarik/vundle.git', here('_vim/bundle/vundle')]) != 0:
if input('Error getting Vundle. Continue setup? [y/N]') not in ('y', 'Y'):
return 1
global backup
backup = input('Delete existing files (no backs them up)? [y/N]: ') not in ('y', 'Y')
here_to_home('bash')
bashrc = eu('~/.bashrc')
bashappend = open('_bashrc.append').read()
try:
if bashappend not in open(bashrc).read():
with open(bashrc, 'a') as f:
f.write(bashappend)
except IOError:
# Assume non-existing file. Create one.
# (Or no permission, this wont change anything in that case.)
with open(bashrc, 'w+') as f:
f.write(bashappend)
here_to_home('vimrc')
here_to_home('vim')
here_to_home('tmux.conf')
here_to_home('inputrc')
here_to_home('Xresources')
here_to_home('gitconfig')
here_to_home('gitignore')
here_to_home('pythonrc.py')
here_to_home('juliarc.jl')
here_to_home('ssh_config', 'ssh/config', symbolic=False) # Can't be symlink due to permissions.
here_to_home('config/awesome')
here_to_home('config/htop')
# Disabled ones don't seem to work.
nb_ext(['autoscroll.js'], enable=False)
nb_ext(['breakpoints.js'], enable=False)
nb_ext(['init_cell.js'])
nb_ext(['notify.js'])
nb_ext(['main.js', 'button.png'], 'equation_numbering')
nb_ext(['ExecuteTime.js', 'ExecuteTime.css'], 'execute_time')
nb_ext(['main.js', 'main.css'], 'toc')
from distutils import spawn
if spawn.find_executable('fish'):
here_to_home('config/fish/solarized.fish')
here_to_home('config/fish/config.fish')
here_to_home('config/fish/functions/fish_prompt.fish')
here_to_home('config/fish/functions/grolschnext.fish')
here_to_home('config/fish/functions/grolschpp.fish')
here_to_home('config/fish/functions/grolschprev.fish')
else:
print("WARNING: skipped fish, it seems not to be installed.")
# Reload some stuff
if 'DISPLAY' in os.environ:
call(['xrdb', '-nocpp', '-merge', '~/.Xresources'], shell=True)
print("Don't forget to possibly run the following: ")
print("- Open vim and run `:BundleInstall` or `:BundleUpdate`")
print("- `cd _vim/bundle/YouCompleteMe/` and `python install.py --clang-completer/--all`")
parser.add_argument('-dg','--drop-zero-sig-genes',action='store_true',help='Drop any gene that is not expressed in any cellular signals from the fit. With a zero intercept, these genes would add an infinite contribution to the log-likelihood. So the main way this changes is the fit is via the goodness-of-fit metric and possibly the size of the required intercept term if there are many such genes.')
parser.add_argument('-ie','--init-log-exposure',type=float,help='Initial value of log-exposure to use when training model. A moderately negative value helps speed up the fit. If set too far from 0 the fit will fail to find a sensible solution.',default=-10)
parser.add_argument('-r','--learn-rate',type=float,help='The learn rate to use.',default=0.01)
parser.add_argument('-p','--poll-interval',type=int,help='Poll fit after this many iterations',default=100)
parser.add_argument('--max-it',type=int,help='Maximum number of iterations',default=1e7)
parser.add_argument('-tl','--log-likelihood-tolerance',type=float,help='Termination condition. Stop when improvement in the log-likelihood less than this.',default=1e-6)
parser.add_argument('-ts','--sparsity-tolerance',type=float,help='Termination condition. Stop when improvement in the sparsity is less than this.',default=1e-4)
args = parser.parse_args()
###################
# Save parameters #
###################
print("Launching deconvolution with arguments:")
print(args)
tmp = vars(args)
args.output = eu(args.output)
with open(args.output+'_arguements.tsv','w') as f:
x = f.write('Parameter\tValue\n')
x = f.write('Launched\t'+str(datetime.datetime.now())+'\n')
x = f.write('WorkDir\t'+os.getcwd()+'\n')
for k in tmp.keys():
x = f.write(k+'\t')
x = f.write(str(tmp[k])+'\n')
##################
# Load bulk data #
##################
#Determine list of files to load
#Go through them one at a time and either parse the file list or store the path
bulkSrcs = []
def autostart():
script = eu("~/.config/qtile/autostart.sh")
subprocess.call([script])
def compressuser(path):
from os.path import expanduser as eu
if path.startswith(eu('~').lower()):
return path.replace(eu('~').lower(),"~",1)
return path
If this cell works, then you have all the requirements for this tutorial installed correctly! """ import numpy as np import pylab as plt %matplotlib inline """ Adding the location of the library should only be necessary if you haven't already added GPy to your PYTHONPATH """ from os.path import expanduser as eu import sys # Change this to your GPy installation location GPy_path = '~/DPhil/Code/libraries/GPy' sys.path.append(eu(GPy_path)) import GPy # <codecell> #Misc settings fs = (9, 5) # figure size; change this if you need to ms = 11 # marker size in plots sd = 6 # random seed # <markdowncell> # ##Kernels # The workhorse of the Gaussian Process is the kernel. This defines the relationship between points and contains any prior knowledge of the domain: #
#!/usr/bin/env python
import os
from os.path import expanduser as eu
display_list = eu('~/.config/i3/displays')
last_external = eu('~/.config/i3/last_ext')
lid = eu('~/.config/i3/lid')
os.system('xrandr >{0}'.format(display_list))
os.system('cat /proc/acpi/button/lid/LID0/state >{0}'.format(lid))
displays = 0
for line in open(lid):
line = line.rstrip().split()
if line[1] == 'closed':
lid_open = False
else:
lid_open = True
print(lid_open)
resolutions = []
IDs = []
conn = False
for line in open(display_list):
line = line.rstrip()
if ' connected ' in line:
id = line.split()[0]
if id == 'eDP1':
continue
params = params.parse_args()
# parse fasta aln
fdat = {k:translatedDNA(v) for k, v in parsefasta(params.fa).items()}
# parse fo subtype
try:
subtype = re.search('(H3N2|pH1N1|H1N1pdm09|BVic|BYam)', params.input_file).group()
aln_subtype = {'H3N2':'H3', 'pH1N1':'pH1abs', 'H1N1pdm09':'pH1abs', 'BVic':'B73', 'BYam':'B73'}[subtype]
except:
raise Exception('Can\'t parse for aln_subtype.')
# copy structure file into current working directory
# only H3 is chains = 2
struc_file = {'H3N2':'4we8_Vic11_Repair.pdb', 'H1N1pdm09':'4jtv_Repair.pdb', 'BVic':'4fqm_Repair.pdb', 'BYam':'4m44_Repair.pdb'}[subtype]
struc_dir = eu('~/Dropbox/age_final_submission/ageflu/files/')
cmd = 'cp {}{} ./'.format(struc_dir, struc_file)
subprocess.call(cmd, shell=True)
# parse input file
fhandle = filter(None, open(params.input_file, 'rU').readlines())
all_mutation_list = []
pt_to_charge_change_count = {}
pt_to_mutation_count = {}
pt_to_glyco_change_count = {}
pos_to_pt_glycogainloss_count = {}
for line in fhandle:
line = line.strip().split('\t')
import json, sys, os
from os.path import expanduser as eu
from hac import GreedyAgglomerativeClusterer
import networkx as nx
from collections import defaultdict
# # Clustering!
# In this notebook, we perform the actual clustering. Given an input scenario, we:
# 1. perform all possible clusterings, from 1 to $\min\{|\mathcal{V},|,|\mathcal{H}|\}$;
# 2. for each possible clustering, check if a _straightforward_ clustering, where bigger VNF clusters are associated with bigger host clusters, is _prima facie_ feasible.
#
# The path of input and output files (both in JSON) are specified as environment variables.
# In[31]:
input_path = os.getenv('INPUT_PATH', eu('test/release1/test_req.json'))
output_path = os.getenv('OUTPUT_PATH',
eu('test/release1/test_req_cluster_decisions.json'))
# First things first, we build two graphs, one for VNFs and one for VNF. Weights are:
# * for the VNF graph, the traffic between VNFs;
# * for the host graph, the capacity of links.
# In[32]:
def cluster(PARequest):
"""Executes the clustering of the PARequest
:PARequest: REST API PARequest
:returns: PARequest dictionary with the clustering decisions
#!/usr/bin/env python
import os, sys
from os.path import expanduser as eu
sinks = eu('~/.config/i3/sinks')
os.system('pactl list sinks >{0}'.format(sinks))
action = sys.argv[1]
last_sink = '0'
for line in open(sinks):
line = line.rstrip()
if 'Sink ' in line:
last_sink = line.split('Sink #')[1]
if 'alsa_output.pci-0000_00_1f.3.analog-stereo' in line:
if action == 'inc':
os.system('pactl set-sink-volume {0} +5%'.format(last_sink))
if action == 'dec':
os.system('pactl set-sink-volume {0} -5%'.format(last_sink))
if action == 'mute':
os.system('pactl set-sink-mute {0} toggle'.format(last_sink))
sys.exit()