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import torch import random import struct from torch import nn from torch.utils.data import TensorDataset, DataLoader from typing import Union def binary_float(num: float, network=True) -> list[float]: """Convert a float to a 32-long list of bits according to IEEE 754. :param: num number to be converted, must be float :param: network format in network byte order, i.e. big endian. Default True. :returns: list of float, either 1.0f or 0.0f (this is because Pytorch uses float tensors) """ fmt = '!f' if network else 'f' bitstring = ''.join(bin(c).replace('0b', '').rjust(8, '0') for c in struct.pack(fmt, num)) return [float(bit) for bit in bitstring]
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import os import pygame from config import DIR_FRAMES_POTENTIAL, DIR_FRAMES_SIGNS, DIR_CROPPED_SIGNS, DIR_FRAMES_NO_SIGNS, IMAGE_HEIGHT, IMAGE_WIDTH, IMAGES_PER_SECOND, CROPPED_SIZE from window import Window, get_rnd_filename, save_cropped if __name__ == "__main__": main()
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########################################################################### # # Copyright 2020 Google LLC # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # ########################################################################### from random import choice from googleapiclient import discovery from django.db import models from django.conf import settings from django.contrib.auth.models import BaseUserManager, AbstractBaseUser from starthinker.util.auth_wrapper import CredentialsUserWrapper from starthinker_ui.account.apps import USER_BUCKET
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#!/usr/bin/python3.4 import socket import pickle import struct import serial import time from datetime import datetime import sys import math import snap7 client = snap7.client.Client() client.connect('137.138.192.181', 0, 0) topo = client.db_read(402,36,1) topo2 = client.db_read(402,44,1) print(hex(topo[0]), hex(topo2[0])) print(topo[0]&0b00001, topo2[0]&0b00001) #for probe in probes: # byte_index=probes[probe] # x = topo[byte_index:byte_index + 4] # temps[probe] = struct.unpack('>f', struct.pack('4B', *x))[0]
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from django.test import TestCase, override_settings from switchboard.mailer import generate_message TEST_EMAIL_FROM_ADDRESS='[email protected]' @override_settings(EMAIL_FROM_ADDRESS=TEST_EMAIL_FROM_ADDRESS)
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# ex:ts=4:sw=4:sts=4:et # -*- tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- """ BitBake Utility Functions """ # Copyright (C) 2004 Michael Lauer # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License version 2 as # published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License along # with this program; if not, write to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. import re, fcntl, os, string, stat, shutil, time import sys import errno import logging import bb import bb.msg import multiprocessing import fcntl import subprocess import glob import traceback import errno from commands import getstatusoutput from contextlib import contextmanager logger = logging.getLogger("BitBake.Util") # Context used in better_exec, eval _context = clean_context() def split_version(s): """Split a version string into its constituent parts (PE, PV, PR)""" s = s.strip(" <>=") e = 0 if s.count(':'): e = int(s.split(":")[0]) s = s.split(":")[1] r = "" if s.count('-'): r = s.rsplit("-", 1)[1] s = s.rsplit("-", 1)[0] v = s return (e, v, r) def explode_deps(s): """ Take an RDEPENDS style string of format: "DEPEND1 (optional version) DEPEND2 (optional version) ..." and return a list of dependencies. Version information is ignored. """ r = [] l = s.split() flag = False for i in l: if i[0] == '(': flag = True #j = [] if not flag: r.append(i) #else: # j.append(i) if flag and i.endswith(')'): flag = False # Ignore version #r[-1] += ' ' + ' '.join(j) return r def explode_dep_versions2(s): """ Take an RDEPENDS style string of format: "DEPEND1 (optional version) DEPEND2 (optional version) ..." and return a dictionary of dependencies and versions. """ r = {} l = s.replace(",", "").split() lastdep = None lastcmp = "" lastver = "" incmp = False inversion = False for i in l: if i[0] == '(': incmp = True i = i[1:].strip() if not i: continue if incmp: incmp = False inversion = True # This list is based on behavior and supported comparisons from deb, opkg and rpm. # # Even though =<, <<, ==, !=, =>, and >> may not be supported, # we list each possibly valid item. # The build system is responsible for validation of what it supports. if i.startswith(('<=', '=<', '<<', '==', '!=', '>=', '=>', '>>')): lastcmp = i[0:2] i = i[2:] elif i.startswith(('<', '>', '=')): lastcmp = i[0:1] i = i[1:] else: # This is an unsupported case! lastcmp = (i or "") i = "" i.strip() if not i: continue if inversion: if i.endswith(')'): i = i[:-1] or "" inversion = False if lastver and i: lastver += " " if i: lastver += i if lastdep not in r: r[lastdep] = [] r[lastdep].append(lastcmp + " " + lastver) continue #if not inversion: lastdep = i lastver = "" lastcmp = "" if not (i in r and r[i]): r[lastdep] = [] return r def join_deps(deps, commasep=True): """ Take the result from explode_dep_versions and generate a dependency string """ result = [] for dep in deps: if deps[dep]: if isinstance(deps[dep], list): for v in deps[dep]: result.append(dep + " (" + v + ")") else: result.append(dep + " (" + deps[dep] + ")") else: result.append(dep) if commasep: return ", ".join(result) else: return " ".join(result) def _print_trace(body, line): """ Print the Environment of a Text Body """ error = [] # print the environment of the method min_line = max(1, line-4) max_line = min(line + 4, len(body)) for i in range(min_line, max_line + 1): if line == i: error.append(' *** %.4d:%s' % (i, body[i-1].rstrip())) else: error.append(' %.4d:%s' % (i, body[i-1].rstrip())) return error def better_compile(text, file, realfile, mode = "exec"): """ A better compile method. This method will print the offending lines. """ try: return compile(text, file, mode) except Exception as e: error = [] # split the text into lines again body = text.split('\n') error.append("Error in compiling python function in %s:\n" % realfile) if e.lineno: error.append("The code lines resulting in this error were:") error.extend(_print_trace(body, e.lineno)) else: error.append("The function causing this error was:") for line in body: error.append(line) error.append("%s: %s" % (e.__class__.__name__, str(e))) logger.error("\n".join(error)) e = bb.BBHandledException(e) raise e def better_exec(code, context, text = None, realfile = "<code>"): """ Similiar to better_compile, better_exec will print the lines that are responsible for the error. """ import bb.parse if not text: text = code if not hasattr(code, "co_filename"): code = better_compile(code, realfile, realfile) try: exec(code, get_context(), context) except bb.BBHandledException: # Error already shown so passthrough raise except Exception as e: (t, value, tb) = sys.exc_info() if t in [bb.parse.SkipPackage, bb.build.FuncFailed]: raise try: _print_exception(t, value, tb, realfile, text, context) except Exception as e: logger.error("Exception handler error: %s" % str(e)) e = bb.BBHandledException(e) raise e @contextmanager def fileslocked(files): """Context manager for locking and unlocking file locks.""" locks = [] if files: for lockfile in files: locks.append(bb.utils.lockfile(lockfile)) yield for lock in locks: bb.utils.unlockfile(lock) def lockfile(name, shared=False, retry=True): """ Use the file fn as a lock file, return when the lock has been acquired. Returns a variable to pass to unlockfile(). """ dirname = os.path.dirname(name) mkdirhier(dirname) if not os.access(dirname, os.W_OK): logger.error("Unable to acquire lock '%s', directory is not writable", name) sys.exit(1) op = fcntl.LOCK_EX if shared: op = fcntl.LOCK_SH if not retry: op = op | fcntl.LOCK_NB while True: # If we leave the lockfiles lying around there is no problem # but we should clean up after ourselves. This gives potential # for races though. To work around this, when we acquire the lock # we check the file we locked was still the lock file on disk. # by comparing inode numbers. If they don't match or the lockfile # no longer exists, we start again. # This implementation is unfair since the last person to request the # lock is the most likely to win it. try: lf = open(name, 'a+') fileno = lf.fileno() fcntl.flock(fileno, op) statinfo = os.fstat(fileno) if os.path.exists(lf.name): statinfo2 = os.stat(lf.name) if statinfo.st_ino == statinfo2.st_ino: return lf lf.close() except Exception: try: lf.close() except Exception: pass pass if not retry: return None def unlockfile(lf): """ Unlock a file locked using lockfile() """ try: # If we had a shared lock, we need to promote to exclusive before # removing the lockfile. Attempt this, ignore failures. fcntl.flock(lf.fileno(), fcntl.LOCK_EX|fcntl.LOCK_NB) os.unlink(lf.name) except (IOError, OSError): pass fcntl.flock(lf.fileno(), fcntl.LOCK_UN) lf.close() def md5_file(filename): """ Return the hex string representation of the MD5 checksum of filename. """ try: import hashlib m = hashlib.md5() except ImportError: import md5 m = md5.new() with open(filename, "rb") as f: for line in f: m.update(line) return m.hexdigest() def sha256_file(filename): """ Return the hex string representation of the 256-bit SHA checksum of filename. On Python 2.4 this will return None, so callers will need to handle that by either skipping SHA checks, or running a standalone sha256sum binary. """ try: import hashlib except ImportError: return None s = hashlib.sha256() with open(filename, "rb") as f: for line in f: s.update(line) return s.hexdigest() def preserved_envvars_exported(): """Variables which are taken from the environment and placed in and exported from the metadata""" return [ 'BB_TASKHASH', 'HOME', 'LOGNAME', 'PATH', 'PWD', 'SHELL', 'TERM', 'USER', ] def preserved_envvars(): """Variables which are taken from the environment and placed in the metadata""" v = [ 'BBPATH', 'BB_PRESERVE_ENV', 'BB_ENV_WHITELIST', 'BB_ENV_EXTRAWHITE', ] return v + preserved_envvars_exported() def filter_environment(good_vars): """ Create a pristine environment for bitbake. This will remove variables that are not known and may influence the build in a negative way. """ removed_vars = {} for key in os.environ.keys(): if key in good_vars: continue removed_vars[key] = os.environ[key] os.unsetenv(key) del os.environ[key] if len(removed_vars): logger.debug(1, "Removed the following variables from the environment: %s", ", ".join(removed_vars.keys())) return removed_vars def approved_variables(): """ Determine and return the list of whitelisted variables which are approved to remain in the envrionment. """ if 'BB_PRESERVE_ENV' in os.environ: return os.environ.keys() approved = [] if 'BB_ENV_WHITELIST' in os.environ: approved = os.environ['BB_ENV_WHITELIST'].split() approved.extend(['BB_ENV_WHITELIST']) else: approved = preserved_envvars() if 'BB_ENV_EXTRAWHITE' in os.environ: approved.extend(os.environ['BB_ENV_EXTRAWHITE'].split()) if 'BB_ENV_EXTRAWHITE' not in approved: approved.extend(['BB_ENV_EXTRAWHITE']) return approved def clean_environment(): """ Clean up any spurious environment variables. This will remove any variables the user hasn't chosen to preserve. """ if 'BB_PRESERVE_ENV' not in os.environ: good_vars = approved_variables() return filter_environment(good_vars) return {} def empty_environment(): """ Remove all variables from the environment. """ for s in os.environ.keys(): os.unsetenv(s) del os.environ[s] def build_environment(d): """ Build an environment from all exported variables. """ import bb.data for var in bb.data.keys(d): export = d.getVarFlag(var, "export") if export: os.environ[var] = d.getVar(var, True) or "" def remove(path, recurse=False): """Equivalent to rm -f or rm -rf""" if not path: return if recurse: # shutil.rmtree(name) would be ideal but its too slow subprocess.call(['rm', '-rf'] + glob.glob(path)) return for name in glob.glob(path): try: os.unlink(name) except OSError as exc: if exc.errno != errno.ENOENT: raise # # Could also use return re.compile("(%s)" % "|".join(map(re.escape, suffixes))).sub(lambda mo: "", var) # but thats possibly insane and suffixes is probably going to be small # def mkdirhier(directory): """Create a directory like 'mkdir -p', but does not complain if directory already exists like os.makedirs """ try: os.makedirs(directory) except OSError as e: if e.errno != errno.EEXIST: raise e def movefile(src, dest, newmtime = None, sstat = None): """Moves a file from src to dest, preserving all permissions and attributes; mtime will be preserved even when moving across filesystems. Returns true on success and false on failure. Move is atomic. """ #print "movefile(" + src + "," + dest + "," + str(newmtime) + "," + str(sstat) + ")" try: if not sstat: sstat = os.lstat(src) except Exception as e: print("movefile: Stating source file failed...", e) return None destexists = 1 try: dstat = os.lstat(dest) except: dstat = os.lstat(os.path.dirname(dest)) destexists = 0 if destexists: if stat.S_ISLNK(dstat[stat.ST_MODE]): try: os.unlink(dest) destexists = 0 except Exception as e: pass if stat.S_ISLNK(sstat[stat.ST_MODE]): try: target = os.readlink(src) if destexists and not stat.S_ISDIR(dstat[stat.ST_MODE]): os.unlink(dest) os.symlink(target, dest) #os.lchown(dest,sstat[stat.ST_UID],sstat[stat.ST_GID]) os.unlink(src) return os.lstat(dest) except Exception as e: print("movefile: failed to properly create symlink:", dest, "->", target, e) return None renamefailed = 1 if sstat[stat.ST_DEV] == dstat[stat.ST_DEV]: try: os.rename(src, dest) renamefailed = 0 except Exception as e: if e[0] != errno.EXDEV: # Some random error. print("movefile: Failed to move", src, "to", dest, e) return None # Invalid cross-device-link 'bind' mounted or actually Cross-Device if renamefailed: didcopy = 0 if stat.S_ISREG(sstat[stat.ST_MODE]): try: # For safety copy then move it over. shutil.copyfile(src, dest + "#new") os.rename(dest + "#new", dest) didcopy = 1 except Exception as e: print('movefile: copy', src, '->', dest, 'failed.', e) return None else: #we don't yet handle special, so we need to fall back to /bin/mv a = getstatusoutput("/bin/mv -f " + "'" + src + "' '" + dest + "'") if a[0] != 0: print("movefile: Failed to move special file:" + src + "' to '" + dest + "'", a) return None # failure try: if didcopy: os.lchown(dest, sstat[stat.ST_UID], sstat[stat.ST_GID]) os.chmod(dest, stat.S_IMODE(sstat[stat.ST_MODE])) # Sticky is reset on chown os.unlink(src) except Exception as e: print("movefile: Failed to chown/chmod/unlink", dest, e) return None if newmtime: os.utime(dest, (newmtime, newmtime)) else: os.utime(dest, (sstat[stat.ST_ATIME], sstat[stat.ST_MTIME])) newmtime = sstat[stat.ST_MTIME] return newmtime def copyfile(src, dest, newmtime = None, sstat = None): """ Copies a file from src to dest, preserving all permissions and attributes; mtime will be preserved even when moving across filesystems. Returns true on success and false on failure. """ #print "copyfile(" + src + "," + dest + "," + str(newmtime) + "," + str(sstat) + ")" try: if not sstat: sstat = os.lstat(src) except Exception as e: logger.warn("copyfile: stat of %s failed (%s)" % (src, e)) return False destexists = 1 try: dstat = os.lstat(dest) except: dstat = os.lstat(os.path.dirname(dest)) destexists = 0 if destexists: if stat.S_ISLNK(dstat[stat.ST_MODE]): try: os.unlink(dest) destexists = 0 except Exception as e: pass if stat.S_ISLNK(sstat[stat.ST_MODE]): try: target = os.readlink(src) if destexists and not stat.S_ISDIR(dstat[stat.ST_MODE]): os.unlink(dest) os.symlink(target, dest) #os.lchown(dest,sstat[stat.ST_UID],sstat[stat.ST_GID]) return os.lstat(dest) except Exception as e: logger.warn("copyfile: failed to create symlink %s to %s (%s)" % (dest, target, e)) return False if stat.S_ISREG(sstat[stat.ST_MODE]): try: srcchown = False if not os.access(src, os.R_OK): # Make sure we can read it srcchown = True os.chmod(src, sstat[stat.ST_MODE] | stat.S_IRUSR) # For safety copy then move it over. shutil.copyfile(src, dest + "#new") os.rename(dest + "#new", dest) except Exception as e: logger.warn("copyfile: copy %s to %s failed (%s)" % (src, dest, e)) return False finally: if srcchown: os.chmod(src, sstat[stat.ST_MODE]) os.utime(src, (sstat[stat.ST_ATIME], sstat[stat.ST_MTIME])) else: #we don't yet handle special, so we need to fall back to /bin/mv a = getstatusoutput("/bin/cp -f " + "'" + src + "' '" + dest + "'") if a[0] != 0: logger.warn("copyfile: failed to copy special file %s to %s (%s)" % (src, dest, a)) return False # failure try: os.lchown(dest, sstat[stat.ST_UID], sstat[stat.ST_GID]) os.chmod(dest, stat.S_IMODE(sstat[stat.ST_MODE])) # Sticky is reset on chown except Exception as e: logger.warn("copyfile: failed to chown/chmod %s (%s)" % (dest, e)) return False if newmtime: os.utime(dest, (newmtime, newmtime)) else: os.utime(dest, (sstat[stat.ST_ATIME], sstat[stat.ST_MTIME])) newmtime = sstat[stat.ST_MTIME] return newmtime def which(path, item, direction = 0, history = False): """ Locate a file in a PATH """ hist = [] paths = (path or "").split(':') if direction != 0: paths.reverse() for p in paths: next = os.path.join(p, item) hist.append(next) if os.path.exists(next): if not os.path.isabs(next): next = os.path.abspath(next) if history: return next, hist return next if history: return "", hist return "" # # Was present to work around multiprocessing pool bugs in python < 2.7.3 #
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2.122867
9,376
#!/usr/bin/env python import time import argparse import os import socket import math import numpy as np from icecube import (dataio, tableio, astro, toprec, dataclasses, icetray, phys_services, stochastics, millipede, ddddr) from icecube.frame_object_diff.segments import uncompress from I3Tray import * from icecube.tableio import I3TableWriter from icecube.hdfwriter import I3HDFTableService from icecube.icetop_Level3_scripts.functions import count_stations from icecube import icetop_Level3_scripts, stochastics, dataclasses, millipede, photonics_service, ddddr, STTools from icecube.icetop_Level3_scripts.segments import EnergylossReco import comptools as comp import icetray_software def validate_i3_files(files): """ Checks that input i3 files aren't corrupted Parameters ---------- files : array-like Iterable of i3 file paths to check. Returns ------- good_file_list : list List of i3 files (from input files) that were able to be succeessfully loaded. """ if isinstance(files, str): files = [files] good_file_list = [] for i3file in files: try: test_tray = I3Tray() test_tray.Add('I3Reader', FileName=i3file) test_tray.Add(uncompress, 'uncompress') test_tray.Execute() test_tray.Finish() good_file_list.append(i3file) except RuntimeError: icetray.logging.log_warn('File {} is truncated'.format(i3file)) finally: del test_tray return good_file_list def check_keys(frame, *keys): """ Function to check if all keys are in frame Parameters ---------- frame : I3Frame I3Frame keys: Series of keys to look for in frame Returns ------- boolean Whether or not all the keys in keys are in frame """ return all([key in frame for key in keys]) def delete_keys(frame, keys): """ Deletes existing keys in an I3Frame Parameters ---------- frame : I3Frame I3Frame keys: Iterable of keys to delete """ if isinstance(keys, str): keys = [keys] for key in keys: if key in frame: frame.Delete(key) if __name__ == '__main__': description='Runs extra modules over a given fileList' parser = argparse.ArgumentParser(description=description) parser.add_argument('-f', '--files', dest='files', nargs='*', help='Files to run over') parser.add_argument('--type', dest='type', choices=['data', 'sim'], default='sim', help='Option to process simulation or data') parser.add_argument('--sim', dest='sim', help='Simulation dataset') parser.add_argument('--snow_lambda', dest='snow_lambda', type=float, help='Snow lambda to use with Laputop reconstruction') parser.add_argument('--dom_eff', dest='dom_eff', type=float, help='DOM efficiency to use with Millipede reconstruction') parser.add_argument('-o', '--outfile', dest='outfile', help='Output file') args = parser.parse_args() # Starting parameters IT_pulses, inice_pulses = comp.datafunctions.reco_pulses() # Keys to write to frame keys = [] if args.type == 'sim': keys += ['MCPrimary'] keys += ['FractionContainment_MCPrimary_IceTop', 'FractionContainment_MCPrimary_InIce'] keys += ['tanks_charge_Laputop', 'tanks_dist_Laputop'] # Keys read directly from level3 processed i3 files keys += ['I3EventHeader'] keys += ['IceTopMaxSignal', 'IceTopMaxSignalString', 'IceTopMaxSignalInEdge', 'IceTopNeighbourMaxSignal', 'StationDensity'] keys += ['Laputop', 'LaputopParams'] keys += ['Stoch_Reco', 'Stoch_Reco2', 'MillipedeFitParams'] keys += ['I3MuonEnergyLaputopParams'] # Keys that are added to the frame keys += ['NStations'] keys += ['avg_inice_radius', 'std_inice_radius', 'median_inice_radius', 'frac_outside_one_std_inice_radius', 'frac_outside_two_std_inice_radius'] dom_numbers = [1, 15, 30, 45, 60] for min_DOM, max_DOM in zip(dom_numbers[:-1], dom_numbers[1:]): key = '{}_{}'.format(min_DOM, max_DOM) keys += ['NChannels_'+key, 'NHits_'+key, 'InIce_charge_'+key, 'max_qfrac_'+key, ] key = '1_60' keys += ['NChannels_'+key, 'NHits_'+key, 'InIce_charge_'+key, 'max_qfrac_'+key, ] keys += ['FractionContainment_Laputop_IceTop', 'FractionContainment_Laputop_InIce'] keys += ['lap_fitstatus_ok'] keys += ['passed_IceTopQualityCuts', 'passed_InIceQualityCuts'] keys += ['angle_MCPrimary_Laputop'] t0 = time.time() icetray.set_log_level(icetray.I3LogLevel.LOG_WARN) comp.check_output_dir(args.outfile) with comp.localized(inputs=args.files, output=args.outfile) as (inputs, output): # Construct list of non-truncated files to process good_file_list = validate_i3_files(inputs) tray = I3Tray() tray.Add('I3Reader', FileNameList=good_file_list) # Uncompress Level3 diff files tray.Add(uncompress, 'uncompress') if args.snow_lambda is not None: # Re-run Laputop reconstruction with specified snow correction lambda value tray = icetray_software.rerun_reconstructions_snow_lambda(tray, snow_lambda=args.snow_lambda) if args.dom_eff is not None: delete_keys = ['Millipede', 'MillipedeFitParams', 'Stoch_Reco', 'Stoch_Reco2', 'Millipede_dEdX', 'I3MuonEnergyLaputopParams', 'I3MuonEnergyLaputopCascadeParams', 'IT73AnalysisInIceQualityCuts', ] tray.Add('Delete', keys=delete_keys) from icecube.icetop_Level3_scripts import icetop_globals # from icecube.icetop_Level3_scripts.segments import muonReconstructions from icecube.icetop_Level3_scripts.modules import MakeQualityCuts name = 'reco' spline_dir="/data/sim/sim-new/downloads/spline-tables/" inice_clean_coinc_pulses = icetop_globals.inice_clean_coinc_pulses tray.AddSegment(EnergylossReco, name+'_ElossReco', InIcePulses=inice_clean_coinc_pulses, dom_eff=args.dom_eff, splinedir=spline_dir, IceTopTrack='Laputop', If=lambda fr: "NCh_"+inice_clean_coinc_pulses in fr and fr['NCh_' + inice_clean_coinc_pulses].value ) # Collect in IT73AnalysisInIceQualityCuts CutOrder = ["NCh_"+inice_clean_coinc_pulses, "MilliRlogl", "MilliQtot", "MilliNCasc", "StochReco"] CutsToEvaluate={"NCh_"+inice_clean_coinc_pulses:(lambda fr: fr["NCh_"+inice_clean_coinc_pulses].value), "MilliRlogl":(lambda fr: "MillipedeFitParams" in fr and math.log10(fr["MillipedeFitParams"].rlogl)<2), "MilliQtot": (lambda fr: "MillipedeFitParams" in fr and math.log10(fr["MillipedeFitParams"].predicted_qtotal/fr["MillipedeFitParams"].qtotal)>-0.03), "MilliNCasc": (lambda fr: "Millipede_dEdX" in fr and len([part for part in fr["Millipede_dEdX"] if part.energy > 0]) >= 3), "StochReco": (lambda fr: "Stoch_Reco" in fr and fr["Stoch_Reco"].status == dataclasses.I3Particle.OK)} CutsNames={"NCh_"+inice_clean_coinc_pulses:"NCh_"+inice_clean_coinc_pulses+"Above7", "MilliRlogl":"MilliRloglBelow2", "MilliQtot":"MilliQtotRatio", "MilliNCasc":"MilliNCascAbove2", "StochReco":"StochRecoSucceeded"} tray.AddModule(MakeQualityCuts, name+'_DoInIceCuts', RemoveEvents=False, CutOrder=CutOrder, CutsToEvaluate=CutsToEvaluate, CutsNames=CutsNames, CollectBools="IT73AnalysisInIceQualityCuts" ) if args.type == 'data': # Filter out all events that don't pass standard IceTop cuts tray.Add(lambda frame: all(frame['IT73AnalysisIceTopQualityCuts'].values())) # Filter out non-coincident P frames tray.Add(lambda frame: inice_pulses in frame) tray.Add(icetray_software.add_IceTop_quality_cuts, If=lambda frame: 'IT73AnalysisIceTopQualityCuts' in frame) tray.Add(icetray_software.add_InIce_quality_cuts, If=lambda frame: 'IT73AnalysisInIceQualityCuts' in frame) tray.Add(icetray_software.add_nstations, pulses=IT_pulses, If=lambda frame: IT_pulses in frame) # Add total inice charge to frame for min_DOM, max_DOM in zip(dom_numbers[:-1], dom_numbers[1:]): tray.Add(icetray_software.AddInIceCharge, pulses=inice_pulses, min_DOM=min_DOM, max_DOM=max_DOM, If=lambda frame: 'I3Geometry' in frame and inice_pulses in frame) tray.Add(icetray_software.AddInIceCharge, pulses=inice_pulses, min_DOM=1, max_DOM=60, If=lambda frame: 'I3Geometry' in frame and inice_pulses in frame) # Add InIce muon radius to frame tray.Add(icetray_software.AddInIceMuonRadius, track='Laputop', pulses='CoincLaputopCleanedPulses', min_DOM=1, max_DOM=60, If=lambda frame: check_keys(frame, 'I3Geometry', 'Laputop', 'CoincLaputopCleanedPulses') ) # Add fraction containment to frame tray.Add(icetray_software.add_fraction_containment, track='Laputop', If=lambda frame: check_keys(frame, 'I3Geometry', 'Laputop') ) # if args.type == 'sim': tray.Add(icetray_software.add_fraction_containment, track='MCPrimary', If=lambda frame: check_keys(frame, 'I3Geometry', 'MCPrimary') ) # Add Laputop fitstatus ok boolean to frame tray.Add(icetray_software.lap_fitstatus_ok, If=lambda frame: 'Laputop' in frame) # Add opening angle between Laputop and MCPrimary for angular resolution calculation tray.Add(icetray_software.add_opening_angle, particle1='MCPrimary', particle2='Laputop', key='angle_MCPrimary_Laputop', If=lambda frame: 'MCPrimary' in frame and 'Laputop' in frame) #==================================================================== # Finish hdf = I3HDFTableService(output) keys = {key: tableio.default for key in keys} if args.type == 'data': keys['Laputop'] = [dataclasses.converters.I3ParticleConverter(), astro.converters.I3AstroConverter()] tray.Add(I3TableWriter, tableservice=hdf, keys=keys, SubEventStreams=['ice_top']) tray.Execute() tray.Finish() print('Time taken: {}'.format(time.time() - t0))
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# Copyright 2018 - Vitrage team # # Licensed under the Apache License, Version 2.0 (the "License"); you may # not use this file except in compliance with the License. You may obtain # a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, WITHOUT # WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the # License for the specific language governing permissions and limitations # under the License. from oslo_log import log from vitrage.datasources.driver_base import DriverBase from vitrage.datasources.sample import SAMPLE_DATASOURCE LOG = log.getLogger(__name__)
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from timemachines.skatertools.testing.allregressiontests import REGRESSION_TESTS import time import random TIMEOUT = 60*5 # Regression tests run occasionally to check various parts of hyper-param spaces, etc. if __name__=='__main__': start_time = time.time() elapsed = time.time()-start_time while elapsed < TIMEOUT: a_test = random.choice(REGRESSION_TESTS) print('Running '+str(a_test.__name__)) a_test() elapsed = time.time() - start_time
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#!/usr/bin/python """A script for manual testing and experimenting with the ks server. TODO(jlewi): Should we use this as the basis for doing E2E integration testing? We can run the server in a subprocess. Send requests to it and then run various checks on the results. """ import argparse import datetime import logging import requests if __name__ == "__main__": logging.basicConfig(level=logging.INFO, format=('%(levelname)s|%(asctime)s' '|%(pathname)s|%(lineno)d| %(message)s'), datefmt='%Y-%m-%dT%H:%M:%S', ) logging.getLogger().setLevel(logging.INFO) main()
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import glob import numpy as np import time import zarr import torch import torch.utils.data as data
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# Copyright (c) Microsoft Corporation. All rights reserved. # Licensed under the MIT license. import torch import torch.nn as nn import torch.autograd as autograd class CRFLoss(nn.Module): """CRFLoss use for crf output layer for sequence tagging task. """ def _score_sentence(self, scores, mask, tags, transitions, crf_layer_conf): """ input: scores: variable (seq_len, batch, tag_size, tag_size) mask: (batch, seq_len) tags: tensor (batch, seq_len) output: score: sum of score for gold sequences within whole batch """ # Gives the score of a provided tag sequence batch_size = scores.size(1) seq_len = scores.size(0) tag_size = scores.size(2) # convert tag value into a new format, recorded label bigram information to index new_tags = autograd.Variable(torch.LongTensor(batch_size, seq_len)) if crf_layer_conf.use_gpu: new_tags = new_tags.cuda() for idx in range(seq_len): if idx == 0: # start -> first score new_tags[:, 0] = (tag_size-2)*tag_size + tags[:, 0] else: new_tags[:, idx] = tags[:, idx-1]*tag_size + tags[:, idx] # transition for label to STOP_TAG end_transition = transitions[:, crf_layer_conf.target_dict[crf_layer_conf.STOP_TAG]].contiguous().view(1, tag_size).expand(batch_size, tag_size) # length for batch, last word position = length - 1 length_mask = torch.sum(mask.long(), dim=1).view(batch_size, 1).long() # index the label id of last word end_ids = torch.gather(tags, 1, length_mask - 1) # index the transition score for end_id to STOP_TAG end_energy = torch.gather(end_transition, 1, end_ids) # convert tag as (seq_len, batch_size, 1) new_tags = new_tags.transpose(1, 0).contiguous().view(seq_len, batch_size, 1) # need convert tags id to search from positions of scores tg_energy = torch.gather(scores.view(seq_len, batch_size, -1), 2, new_tags).view(seq_len, batch_size) # seq_len * batch_size # mask transpose to (seq_len, batch_size) tg_energy = tg_energy.masked_select(mask.transpose(1, 0)) # add all score together gold_score = tg_energy.sum() + end_energy.sum() return gold_score def forward(self, forward_score, scores, masks, tags, transitions, crf_layer_conf): """ :param forward_score: Tensor scale :param scores: Tensor [seq_len, batch_size, target_size, target_size] :param masks: Tensor [batch_size, seq_len] :param tags: Tensor [batch_size, seq_len] :return: goal_score - forward_score """ gold_score = self._score_sentence(scores, masks, tags, transitions, crf_layer_conf) return forward_score - gold_score
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2.275307
1,304
''' Get sha1 hash of a file or string. usage: sha1sum.py [-h] [-c] [file [file ...]] positional arguments: file String or file to hash. optional arguments: -h, --help show this help message and exit -c, --check Check a file with sha1 hashes and file names for a match. format: sha1_hash filename sha1_hash filename etc. ''' from __future__ import print_function import argparse import os import re import sys import six from Crypto.Hash import SHA ap = argparse.ArgumentParser() ap.add_argument('-c','--check',action='store_true',default=False, help='''Check a file with sha1 hashes and file names for a match. format: hash filename''') ap.add_argument('file',action='store',nargs='*',help='String or file to hash.') args = ap.parse_args(sys.argv[1:]) if args.check: if args.file: s = True for arg in args.file: if os.path.isfile(arg): s = s and check_list(open(arg)) else: s = check_list(make_file(sys.stdin.read())) if s: sys.exit(0) else: sys.exit(1) else: if args.file: for arg in args.file: if os.path.isfile(arg): with open(arg, 'rb') as f: print(get_hash(f)+' '+arg) elif arg == "-": print(get_hash(make_file(sys.stdin.read()))) else: print(get_hash(make_file(arg))) else: print(get_hash(make_file(sys.stdin.read())))
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2.087957
739
# coding=utf-8 """Configuration""" import os SECRET_KEY: str = os.environ.get('SECRET_KEY', 'SUPER_SECRET') PORT: int = int(os.environ.get('PORT', 5000)) DATABASE_URL: str = os.environ.get('RSES_DB_URL') or os.environ.get('DATABASE_URL') # Do you want a flask client RSES_WEB_CLIENT: bool = True
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2.475
120
import quandl import pandas as pd import numpy as np import datetime from sklearn.linear_model import LinearRegression from sklearn import preprocessing, cross_validation df = quandl.get("WIKI/AMZN") df = df[['Adj. Close']] # print(df) # # exit() forecast_out = int(30) # predicting 30 days into future df['Prediction'] = df[['Adj. Close']].shift(-forecast_out) # label column with data shifted 30 units up X = np.array(df.drop(['Prediction'], 1)) X = preprocessing.scale(X) X_forecast = X[-forecast_out:] # set X_forecast equal to last 30 X = X[:-forecast_out] # remove last 30 from X y = np.array(df['Prediction']) y = y[:-forecast_out] X_train, X_test, y_train, y_test = cross_validation.train_test_split(X, y, test_size = 0.2) # Training clf = LinearRegression() clf.fit(X_train,y_train) # Testing confidence = clf.score(X_test, y_test) print("confidence: ", confidence) forecast_prediction = clf.predict(X_forecast) print(forecast_prediction)
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2.680556
360
import logging from itertools import product from force_bdss.api import BaseMCO, DataValue log = logging.getLogger(__name__) def parameter_grid_generator(parameters): """Function to calculate the number of Gromacs experiments required and the combinations of each fragment concentrations""" ranges = [parameter.sample_values for parameter in parameters] for combo in product(*ranges): yield combo def get_labels(parameters): """Generates numerical labels for each categorical MCOParameter""" label_dict = {} label = 1 for parameter in parameters: if hasattr(parameter, "categories"): for name in parameter.categories: if name not in label_dict: label_dict[name] = label label += 1 return label_dict
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2.759076
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# Licensed under a 3-clause BSD style license - see LICENSE.rst from __future__ import division import re import os import logging from pathlib import Path import numpy as np from Chandra.Time import DateTime ORBIT_POINTS_DTYPE = [('date', 'U21'), ('name', 'U8'), ('orbit_num', 'i4'), ('descr', 'U50')] ORBITS_DTYPE = [('orbit_num', 'i4'), ('start', 'U21'), ('stop', 'U21'), ('tstart', 'f8'), ('tstop', 'f8'), ('dur', 'f4'), ('perigee', 'U21'), ('t_perigee', 'f8'), ('apogee', 'U21'), ('start_radzone', 'U21'), ('stop_radzone', 'U21'), ('dt_start_radzone', 'f4'), ('dt_stop_radzone', 'f4')] logger = logging.getLogger('events') MPLOGS_DIR = Path(os.environ['SKA'], 'data', 'mpcrit1', 'mplogs') # Just for reference, all name=descr pairs between 2000 to 2013:001 NAMES = { 'EALT0': 'ALTITUDE ZONE ENTRY0', 'EALT1': 'ALTITUDE ZONE ENTRY 1', 'EALT2': 'ALTITUDE ZONE ENTRY2', 'EALT3': 'ALTITUDE ZONE ENTRY3', 'EAPOGEE': 'ORBIT APOGEE', 'EASCNCR': 'ORBIT ASCENDING NODE CROSSING', 'EE1RADZ0': 'ELECTRON1 RADIATION ENTRY0', 'EE2RADZ0': 'ELECTRON2 RADIATION ENTRY0', 'EEF1000': 'ELECTRON 1 RADIATION ENTRY 0', 'EODAY': 'EARTH SHADOW (UMBRA) EXIT', 'EONIGHT': 'EARTH SHADOW (UMBRA) ENTRY', 'EP1RADZ0': 'PROTON1 RADIATION ENTRY0', 'EP2RADZ0': 'PROTON2 RADIATION ENTRY0', 'EPERIGEE': 'ORBIT PERIGEE', 'EPF1000': 'PROTON 1 RADIATION ENTRY 0', 'EQF003M': 'PROTON FLUX ENTRY FOR ENERGY 0 LEVEL 0 KP 3 MEAN', 'EQF013M': 'PROTON FLUX ENTRY FOR ENERGY 0 LEVEL 1 KP 3 MEAN', 'LSDAY': 'LUNAR SHADOW (UMBRA) EXIT', 'LSNIGHT': 'LUNAR SHADOW (UMBRA) ENTRY', 'LSPENTRY': 'LUNAR SHADOW (PENUMBRA) ENTRY', 'LSPEXIT': 'LUNAR SHADOW (PENUMBRA) EXIT', 'OORMPDS': 'RADMON DISABLE', 'OORMPEN': 'RADMON ENABLE', 'PENTRY': 'EARTH SHADOW (PENUMBRA) ENTRY', 'PEXIT': 'EARTH SHADOW (PENUMBRA) EXIT', 'XALT0': 'ALTITUDE ZONE EXIT 0', 'XALT1': 'ALTITUDE ZONE EXIT 1', 'XALT2': 'ALTITUDE ZONE EXIT2', 'XALT3': 'ALTITUDE ZONE EXIT3', 'XE1RADZ0': 'ELECTRON1 RADIATION EXIT0', 'XE2RADZ0': 'ELECTRON2 RADIATION EXIT0', 'XEF1000': 'ELECTRON 1 RADIATION EXIT 0', 'XP1RADZ0': 'PROTON1 RADIATION EXIT0', 'XP2RADZ0': 'PROTON2 RADIATION EXIT0', 'XPF1000': 'PROTON 1 RADIATION EXIT 0', 'XQF003M': 'PROTON FLUX EXIT FOR ENERGY 0 LEVEL 0 KP 3 MEAN', 'XQF013M': 'PROTON FLUX EXIT FOR ENERGY 0 LEVEL 1 KP 3 MEAN'} def prune_dirs(dirs, regex): """ Prune directories (in-place) that do not match ``regex``. """ prunes = [x for x in dirs if not re.match(regex, x)] for prune in prunes: dirs.remove(prune) # get_tlr_files is slow, so cache results (mostly for testing) get_tlr_files_cache = {} def get_tlr_files(mpdir=''): """ Get all timeline report files within the specified SOT MP directory ``mpdir`` relative to the root of /data/mpcrit1/mplogs. Returns a list of dicts [{name, date},..] """ rootdir = (MPLOGS_DIR / mpdir).absolute() try: return get_tlr_files_cache[rootdir] except KeyError: pass logger.info('Looking for TLR files in {}'.format(rootdir)) tlrfiles = [] for root, dirs, files in os.walk(rootdir): root = root.rstrip('/') depth = len(Path(root).parts) - len(MPLOGS_DIR.parts) logger.debug(f'get_trl_files: root={root} {depth} {rootdir}') if depth == 0: prune_dirs(dirs, r'\d{4}$') elif depth == 1: prune_dirs(dirs, r'[A-Z]{3}\d{4}$') elif depth == 2: prune_dirs(dirs, r'ofls[a-z]$') elif depth > 2: tlrs = [x for x in files if re.match(r'.+\.tlr$', x)] if len(tlrs) == 0: logger.info('NO tlr file found in {}'.format(root)) else: logger.info('Located TLR file {}'.format(os.path.join(root, tlrs[0]))) tlrfiles.append(os.path.join(root, tlrs[0])) while dirs: dirs.pop() files = [] for tlrfile in tlrfiles: monddyy, oflsv = tlrfile.split('/')[-3:-1] mon = monddyy[:3].capitalize() dd = monddyy[3:5] yy = int(monddyy[5:7]) yyyy = 1900 + yy if yy > 95 else 2000 + yy caldate = '{}{}{} at 12:00:00.000'.format(yyyy, mon, dd) files.append((tlrfile, DateTime(caldate).date[:8] + oflsv, DateTime(caldate).date)) files = sorted(files, key=lambda x: x[1]) out = [{'name': x[0], 'date': x[2]} for x in files] get_tlr_files_cache[rootdir] = out return out def prune_a_loads(tlrfiles): """ When there are B or later products, take out the A loads. This is where most mistakes are removed. (CURRENTLY THIS FUNCTION IS NOT USED). """ outs = [] last_monddyy = None for tlrfile in reversed(tlrfiles): monddyy, oflsv = tlrfile.split('/')[-3:-1] if monddyy == last_monddyy and oflsv == 'oflsa': continue else: outs.append(tlrfile) last_monddyy = monddyy return list(reversed(outs)) def filter_known_bad(orbit_points): """ Filter some commands that are known to be incorrect. """ ops = orbit_points bad = np.zeros(len(orbit_points), dtype=bool) bad |= (ops['name'] == 'OORMPEN') & (ops['date'] == '2002:253:10:08:52.239') bad |= (ops['name'] == 'OORMPEN') & (ops['date'] == '2004:010:10:00:00.000') return orbit_points[~bad] def get_orbit_points(tlrfiles): """ Get all orbit points from the timeline reports within the specified mission planning path '' (all) or 'YYYY' (year) or YYYY/MONDDYY (load). """ orbit_points = [] # tlrfiles = prune_a_loads(tlrfiles) for tlrfile in tlrfiles: # Parse thing like this: # 2012:025:21:22:21.732 EQF013M 1722 PROTON FLUX ENTRY FOR ENERGY 0 LEVEL ... # 012345678901234567890123456789012345678901234567890123456789 logger.info('Getting points from {}'.format(tlrfile)) try: fh = open(tlrfile, 'r', encoding='ascii', errors='ignore') except IOError as err: logger.warn(err) continue for line in fh: if len(line) < 30 or line[:2] != ' 2': continue try: date, name, orbit_num, descr = line.split(None, 3) except ValueError: continue if name.startswith('OORMP'): orbit_num = -1 descr = 'RADMON {}ABLE'.format('EN' if name.endswith('EN') else 'DIS') elif line[23] in ' -': continue if 'DSS-' in name: continue if not re.match(r'\d{4}:\d{3}:\d{2}:\d{2}:\d{2}\.\d{3}', date): logger.info('Failed for date: "{}"'.format(date)) continue if not re.match(r'[A-Z]+', name): logger.info('Failed for name: "{}"'.format(name)) continue try: orbit_num = int(orbit_num) except TypeError: logger.info('Failed for orbit_num: {}'.format(orbit_num)) continue descr = descr.strip() orbit_points.append((date, name, orbit_num, descr)) orbit_points = sorted(set(orbit_points), key=lambda x: x[0]) return orbit_points def get_nearest_orbit_num(orbit_nums, idx, d_idx): """ Get the orbit number nearest to ``orbit_nums[idx]`` in direction ``d_idx``, skipping values of -1 (from radmon commanding). """ while True: idx += d_idx if idx < 0 or idx >= len(orbit_nums): raise NotFoundError('No nearest orbit num found') if orbit_nums[idx] != -1: break return orbit_nums[idx], idx def interpolate_orbit_points(orbit_points, name): """ Linearly interpolate across any gaps for ``name`` orbit_points. """ if len(orbit_points) == 0: return [] ok = orbit_points['name'] == name ops = orbit_points[ok] # Get the indexes of missing orbits idxs = np.flatnonzero(np.diff(ops['orbit_num']) > 1) new_orbit_points = [] for idx in idxs: op0 = ops[idx] op1 = ops[idx + 1] orb_num0 = op0['orbit_num'] orb_num1 = op1['orbit_num'] time0 = DateTime(op0['date']).secs time1 = DateTime(op1['date']).secs for orb_num in range(orb_num0 + 1, orb_num1): time = time0 + (orb_num - orb_num0) / (orb_num1 - orb_num0) * (time1 - time0) date = DateTime(time).date new_orbit_point = (date, name, orb_num, op0['descr']) logger.info('Adding new orbit point {}'.format(new_orbit_point)) new_orbit_points.append(new_orbit_point) return new_orbit_points def process_orbit_points(orbit_points): """ Take the raw orbit points (list of tuples) and do some processing: - Remove duplicate events within 30 seconds of each other - Fill in orbit number for RADMON enable / disable points - Convert to a number structured array Returns a numpy array with processed orbit points:: ORBIT_POINTS_DTYPE = [('date', 'U21'), ('name', 'U8'), ('orbit_num', 'i4'), ('descr', 'U50')] """ # Find neighboring pairs of orbit points that are identical except for date. # If the dates are then within 180 seconds of each other then toss the first # of the pair. if len(orbit_points) == 0: return np.array([], dtype=ORBIT_POINTS_DTYPE) uniq_orbit_points = [] for op0, op1 in zip(orbit_points[:-1], orbit_points[1:]): if op0[1:4] == op1[1:4]: dt = (DateTime(op1[0]) - DateTime(op0[0])) * 86400 if dt < 180: # logger.info('Removing duplicate orbit points:\n {}\n {}' # .format(str(op0), str(op1))) continue uniq_orbit_points.append(op1) uniq_orbit_points.append(orbit_points[-1]) orbit_points = uniq_orbit_points # Convert to a numpy structured array orbit_points = np.array(orbit_points, dtype=ORBIT_POINTS_DTYPE) # Filter known bad points orbit_points = filter_known_bad(orbit_points) # For key orbit points linearly interpolate across gaps in orbit coverage. new_ops = [] for name in ('EPERIGEE', 'EAPOGEE', 'EASCNCR'): new_ops.extend(interpolate_orbit_points(orbit_points, name)) # Add a new orbit point for the ascending node EXIT which is the end of each orbit. # This simplifies bookkeeping later. for op in orbit_points[orbit_points['name'] == 'EASCNCR']: new_ops.append((op['date'], 'XASCNCR', op['orbit_num'] - 1, op['descr'] + ' EXIT')) # Add corresponding XASCNCR for any new EASCNCR points for op in new_ops: if op[1] == 'EASCNCR': new_ops.append((op[0], 'XASCNCR', op[2] - 1, op[3] + ' EXIT')) logger.info('Adding {} new orbit points'.format(len(new_ops))) new_ops = np.array(new_ops, dtype=ORBIT_POINTS_DTYPE) orbit_points = np.concatenate([orbit_points, new_ops]) orbit_points.sort(order=['date', 'orbit_num']) # Fill in orbit number for RADMON enable / disable points radmon_idxs = np.flatnonzero(orbit_points['orbit_num'] == -1) orbit_nums = orbit_points['orbit_num'] for idx in radmon_idxs: try: prev_num, prev_idx = get_nearest_orbit_num(orbit_nums, idx, -1) next_num, next_idx = get_nearest_orbit_num(orbit_nums, idx, +1) except NotFoundError: logger.info('No nearest orbit point for orbit_points[{}] (len={})' .format(idx, len(orbit_points))) else: if prev_num == next_num: orbit_nums[idx] = next_num else: logger.info('Unable to assign orbit num idx={} prev={} next={}' .format(idx, prev_num, next_num)) logger.info(' {} {}'.format(prev_idx, orbit_points[prev_idx])) logger.info(' * {} {}'.format(idx, orbit_points[idx])) logger.info(' {} {}'.format(next_idx, orbit_points[next_idx])) return orbit_points def get_orbits(orbit_points): """ Collate the orbit points into full orbits, with dates corresponding to start (ORBIT ASCENDING NODE CROSSING), stop, apogee, perigee, radzone start and radzone stop. Radzone is defined as the time covering perigee when radmon is disabled by command. This corresponds to the planned values and may differ from actual in the case of events that run SCS107 and prematurely disable RADMON. Returns a numpy structured array:: ORBITS_DTYPE = [('orbit_num', 'i4'), ('start', 'U21'), ('stop', 'U21'), ('tstart', 'f8'), ('tstop', 'f8'), ('dur', 'f4'), ('perigee', 'U21'), ('t_perigee', 'f8'), ('apogee', 'U21'), ('start_radzone', 'U21'), ('stop_radzone', 'U21'), ('dt_start_radzone', 'f4'), ('dt_stop_radzone', 'f4')] """ def find_radzone(idx_perigee): """ Find the extent of the radiation zone, defined as the last time before perigee that RADMON is enabled until the first time after perigee that RADMON is enabled. """ idx = idx_perigee start_radzone = None while True: idx -= 1 if idx < 0: raise NotFoundError('Did not find RADMON enable prior to {}' .format(orbit_points[idx_perigee])) if orbit_points['name'][idx] == 'OORMPDS': start_radzone = orbit_points['date'][idx] if orbit_points['name'][idx] == 'OORMPEN': if start_radzone is None: raise NotFoundError('Found radmon enable before first disable at idx {}' .format(idx)) break idx = idx_perigee while True: idx += 1 if idx >= len(orbit_points): raise NotFoundError('Did not find RADMON enable after to {}' .format(str(orbit_points[idx_perigee]))) if orbit_points['name'][idx] == 'OORMPEN': stop_radzone = orbit_points['date'][idx] break return start_radzone, stop_radzone # Copy orbit points and sort by orbit_num then date. This allows using # search_sorted to select orbit_points corresponding to each orbit. In # very rare cases (orbit 1448 I think), there are orbit_points that cross # orbit boundaries by a few seconds. This is related to the technique of # reading in every TLR to get maximal coverage of orbit points. orbit_points = orbit_points.copy() orbit_points.sort(order=['orbit_num', 'date']) orbit_nums = orbit_points['orbit_num'] uniq_orbit_nums = sorted(set(orbit_nums[orbit_nums > 0])) orbits = [] for orbit_num in uniq_orbit_nums: i0 = np.searchsorted(orbit_nums, orbit_num, side='left') i1 = np.searchsorted(orbit_nums, orbit_num, side='right') ops = orbit_points[i0: i1] try: if 'EASCNCR' not in ops['name'] or 'XASCNCR' not in ops['name']: raise NotFoundError('Skipping orbit {} incomplete'.format(orbit_num)) start = get_date(ops, 'EASCNCR') stop = get_date(ops, 'XASCNCR') date_apogee = get_date(ops, 'EAPOGEE') date_perigee = get_date(ops, 'EPERIGEE') idx_perigee = get_idx(ops, 'EPERIGEE') + i0 start_radzone, stop_radzone = find_radzone(idx_perigee) except NotFoundError as err: logger.info(err) continue else: dt_radzones = [(DateTime(date) - DateTime(date_perigee)) * 86400.0 for date in (start_radzone, stop_radzone)] tstart = DateTime(start).secs tstop = DateTime(stop).secs orbit = (orbit_num, start, stop, tstart, tstop, tstop - tstart, date_perigee, DateTime(date_perigee).secs, date_apogee, start_radzone, stop_radzone, dt_radzones[0], dt_radzones[1]) logger.info('get_orbits: Adding orbit {} {} {}'.format(orbit_num, start, stop)) orbits.append(orbit) orbits = np.array(orbits, dtype=ORBITS_DTYPE) return orbits def get_radzone_from_orbit(orbit): """ Extract the RadZone fields from an orbit descriptor (which is one row of the orbits structured array). """ start_radzone = DateTime(orbit['start_radzone'], format='date') stop_radzone = DateTime(orbit['stop_radzone'], format='date') tstart = start_radzone.secs tstop = stop_radzone.secs dur = tstop - tstart radzone = {'start': start_radzone.date, 'stop': stop_radzone.date, 'tstart': tstart, 'tstop': tstop, 'dur': dur, 'orbit_num': orbit['orbit_num'], 'perigee': orbit['perigee']} return radzone
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#!/usr/bin/env python """ ZMQ proxy for info queues. Publish Queue: tcp:5550 """ import zmq # these are the ports we are doing proxy for proxies = ['5551'] if __name__ == '__main__': main_proxy_info()
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import pkg_resources, subprocess import os def get_all_pythons(): '''https://stackoverflow.com/a/52123490''' output, err = subprocess.Popen( ['which', '-a', 'python', 'python3','python2'], stdout=subprocess.PIPE, stderr=subprocess.PIPE ).communicate() return output.decode('utf8').split('\n')[:-1]
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""" Augment the dataset according to the loss functions. Input: - a regression data set (x, a, y), which may be obtained using the data_parser - loss function - Theta, a set of thresholds in between 0 and 1 Output: a weighted classification dataset (X, A, Y, W) """ import functools import numpy as np import pandas as pd import data_parser as parser from itertools import repeat import itertools _LOGISTIC_C = 5 def augment_data_ab(X, A, Y, Theta): """ Takes input data and augment it with an additional feature of theta; Return: X tensor_product Theta For absolute loss, we don't do any reweighting. TODO: might add the alpha/2 to match with the write-up """ n = np.shape(X)[0] num_theta = len(Theta) X_aug = pd.concat(repeat(X, num_theta)) A_aug = pd.concat(repeat(A, num_theta)) Y_values = pd.concat(repeat(Y, num_theta)) theta_list = [s for theta in Theta for s in repeat(theta, n)] # Adding theta to the feature X_aug['theta'] = pd.Series(theta_list, index=X_aug.index) Y_aug = Y_values >= X_aug['theta'] Y_aug = Y_aug.map({True: 1, False: 0}) X_aug.index = range(n * num_theta) Y_aug.index = range(n * num_theta) A_aug.index = range(n * num_theta) W_aug = pd.Series(1, Y_aug.index) return X_aug, A_aug, Y_aug, W_aug def augment_data_sq(x, a, y, Theta): """ Augment the dataset so that the x carries an additional feature of theta Then also attach appropriate weights to each data point. Theta: Assume uniform grid Theta """ n = np.shape(x)[0] # number of original data points num_theta = len(Theta) width = Theta[1] - Theta[0] X_aug = pd.concat(repeat(x, num_theta)) A_aug = pd.concat(repeat(a, num_theta)) Y_values = pd.concat(repeat(y, num_theta)) theta_list = [s for theta in Theta for s in repeat(theta, n)] # Adding theta to the feature X_aug['theta'] = pd.Series(theta_list, index=X_aug.index) X_aug.index = range(n * num_theta) # Y_aug.index = range(n * num_theta) A_aug.index = range(n * num_theta) Y_values.index = range(n * num_theta) # two helper functions sq_loss = lambda a, b: (a - b)**2 # square loss function weight_assign = lambda theta, y: (sq_loss(theta + width/2, y) - sq_loss(theta - width/2, y)) W = weight_assign(X_aug['theta'], Y_values) Y_aug = 1*(W < 0) W = abs(W) # Compute the weights return X_aug, A_aug, Y_aug, W def augment_data_logistic(x, a, y, Theta): """ Augment the dataset so that the x carries an additional feature of theta Then also attach appropriate weights to each data point, so that optimize for logisitc loss Theta: Assume uniform grid Theta y: assume the labels are {0, 1} """ n = np.shape(x)[0] # number of original data points num_theta = len(Theta) width = Theta[1] - Theta[0] X_aug = pd.concat(repeat(x, num_theta)) A_aug = pd.concat(repeat(a, num_theta)) Y_values = pd.concat(repeat(y, num_theta)) theta_list = [s for theta in Theta for s in repeat(theta, n)] # Adding theta to the feature X_aug['theta'] = pd.Series(theta_list, index=X_aug.index) X_aug.index = range(n * num_theta) A_aug.index = range(n * num_theta) Y_values.index = range(n * num_theta) # two helper functions logistic_loss = lambda y_hat, y: np.log(1 + np.exp(-(_LOGISTIC_C)*(2 * y - 1) * (2 * y_hat - 1))) / (np.log(1 + np.exp(_LOGISTIC_C))) # re-scaled logistic loss #logistic_loss = lambda y_hat, y: np.log(1 + np.exp(-(_LOGISTIC_C)*(2 * y - 1) * (2 * y_hat - 1))) # re-scaled logistic loss weight_assign = lambda theta, y: (logistic_loss(theta + width/2, y) - logistic_loss(theta - width/2, y)) W = weight_assign(X_aug['theta'], Y_values) Y_aug = 1*(W < 0) W = abs(W) # Compute the weights return X_aug, A_aug, Y_aug, W
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2.329189
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assert unique('aa') == False assert unique('abadkjsld') == False assert unique('aa') == False assert unique('fsl') == True
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# Copyright (C) 2019-2021, TomTom (http://tomtom.com). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """Models of API reference elements.""" from abc import ABC from typing import Dict, List, Optional class ReferableElement(ModelBase): """Base class for all objects that can be referenced/linked to. Attributes: id: Unique identifier, if available. name: Short name of the element. full_name: Fully qualified name. language: Language the element is written in. kind: Kind of language element. """ id: Optional[str] = None name: str = "" full_name: str = "" language: str kind: str = "" class TypeRef(ModelBase): """Reference to a type. Attributes: id: Unique identifier of the type. name: Name of the type. language: Language the type is written in. namespace: Namespace, or package, from which the type is referenced. kind: Kind of language element. prefix: Qualifiers prefixing the type. suffix: Qualifiers suffixing the type. nested: List of nested types. None if no arguments, an empty list if zero arguments. args: Arguments for function like types. None if no arguments, an empty list if zero arguments. returns: Return type in case of closure types. prot: Protection level of the referenced type. """ id: Optional[str] = None name: str language: str namespace: Optional[str] = None kind: Optional[str] = None prefix: Optional[str] = None suffix: Optional[str] = None nested: Optional[List["TypeRef"]] = None args: Optional[List["Parameter"]] = None returns: Optional["TypeRef"] = None prot: Optional[str] = None class Parameter(ModelBase): """Parameter description. Representation of doxygen type paramType Attributes: type: Reference to the type of the parameter. name: Name used for the parameter. description: Explanation of the parameter. default_value: Default value for the parameter. prefix: Prefix for the parameter declaration. """ # doxygen based fields type: Optional[TypeRef] = None name: str = "" description: str = "" default_value: Optional[str] = None prefix: Optional[str] = None class ReturnValueList(ModelBase): """ discrete return value Attributes: name: Value returned . description: Explanation of the name/value. """ # doxygen based fields name: str = "" description: str = "" class ReturnValue(ModelBase): """Value returned from a member. Attributes: type: Reference to the type of return value. description: Explanation of the return value. valuelist: List of possible return values """ type: Optional[TypeRef] = None description: str = "" valuelist: Optional[ReturnValueList] = None class ThrowsClause(ModelBase): """Potential exception thrown from a member. Attributes: type: Reference to the type of the exception. description: Explanation of when the exception is thrown. """ type: TypeRef description: str = "" class Compound(ReferableElement): """Compound object. E.g. a class or enum. Representation of the doxygen type compound. Attributes: members: List of members in the compound. params: List of parameters. exceptions: List of exceptions that can be thrown. returns: Return value. include: Name of the include (file) required to use this compound. namespace: Namespace, or package, the compound is contained in. prot: Protection or visibility level. definition: Full definition in source code. args: All arguments as in source code. initializer: Initial value assignment. brief: Brief description of the compound. description: Full description of the compound. sections: Extra documentation sections with special meanings. static: True if this is marked as static. const: True if this is marked as const. deleted: True if this is marked as deleted. default: True if this is marked as default. constexpr: True if this is marked as constexpr. """ members: List["Compound"] params: List[Parameter] exceptions: List[ThrowsClause] returns: Optional[ReturnValue] = None include: Optional[str] = None namespace: Optional[str] = None prot: str = "" definition: str = "" args: str = "" initializer: str = "" brief: str = "" description: str = "" sections: Dict[str, str] static: bool = False const: bool = False deleted: bool = False default: bool = False constexpr: bool = False
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#!/usr/bin/python # encoding: utf-8 import os import json from time import sleep import signal import requests import re from werkzeug import secure_filename from flask import (Flask, request, render_template, session, redirect, url_for, escape, send_from_directory, Blueprint, abort) new_jp = Blueprint('webhooks', __name__) @new_jp.route('/webhooks', methods=['GET','POST'])
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import os import random import numpy as np import torch import torch.distributed as distributed from torch.nn import SyncBatchNorm from zerovl.models import PIPELINE from zerovl.utils import ENV, build_from_cfg from zerovl.utils import ( is_list_of, logger ) try: from apex.parallel import convert_syncbn_model except ImportError: logger.warning(f'=> ImportError: can not import apex, ' f'distribute training with apex will raise error') __all__ = ['init_device', 'init_resume', 'init_model'] def _load_checkpoint(src_path: str, raise_exception: bool = True): r""" Load checkpoint from local """ if not isinstance(src_path, str): return None if os.path.exists(src_path): return torch.load(src_path, map_location=ENV.device)
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''' tests for the serializers ''' # from django.test import TestCase from unittest import TestCase, main from .serializers import _get_attr_value, UserLDAPSerializer from .models import User from django.conf import settings LDAP_USER_EXAMPLE = ('uid=chiahsuanyang,ou=People,dc=adrf,dc=info', { 'gidNumber': ['502'], 'givenName': ['Chia-Hsuan'], 'homeDirectory': ['/nfshome/chiahsuanyang'], 'loginShell': ['/bin/bash'], 'objectClass': ['inetOrgPerson', 'posixAccount', 'top', 'adrfPerson'], 'uid': ['chiahsuanyang'], 'uidNumber': ['1039'], 'mail': ['[email protected]'], 'sn': ['Yang'], 'cn': ['Chia-Hsuan Yang'], } ) LDAP_PROJECT_EXAMPLE = ('cn=project-Food Analysis,ou=Projects,dc=adrf,dc=info', { 'objectClass': ['posixGroup', 'groupOfMembers', 'adrfProject'], 'summary': ['required field'], 'name': ['Food Analysis'], 'gidNumber': ['7003'], 'creationdate': ['20161130221426Z'], 'cn': ['project-Food Analysis'], 'memberUid': ['rafael', 'will'], } ) LDAP_DFROLE_EXAMPLE = ('cn=annotation-reviewers,ou=Groups,dc=adrf,dc=info', { 'objectClass': ['posixGroup', 'groupOfMembers'], 'gidNumber': ['5004'], 'cn': ['annotation-reviewers'], 'memberUid': ['rafael', 'will'], } ) class LdapSerializersTests(TestCase): ''' Tests for ldap serializers ''' if __name__ == '__main__': main()
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from tkinter import * import tkinter.messagebox as tmsg root = Tk() root.title("Place Order") root.geometry("400x400") scrollbar = Scrollbar(root) scrollbar.pack(side= RIGHT, fill = Y) lbx = Listbox(root, yscrollcommand = scrollbar.set) # lbx.insert(1, "firstItem") # lbx.insert(2, "secondItem") # lbx.insert(3, "thirdItem") # lbx.insert(4, "fourthItem") # lbx.insert(ACTIVE, 0) for i in range(300): lbx.insert(END, "Item {}".format(str(i))) i += 1 scrollbar.config(command = lbx.yview) #to attach the scroll bar to the list, we need to configure it lbx.pack(fill = BOTH) root.mainloop()
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#!/usr/bin/python3 # mari von steinkirch @2013 # steinkirch at gmail import string def delete_unique_word(str1): ''' find and delete all the duplicate characters in a string ''' # create ordered dict table_c = { key : 0 for key in string.ascii_lowercase} # fill the table with the chars in the string for i in str1: table_c[i] += 1 # scan the table to find times chars > 1 for key, value in table_c.items(): if value > 1: str1 = str1.replace(key, "") return str1 if __name__ == '__main__': test_delete_unique_word()
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''' This script solves the exercises of days that have been completed. Jut in case the students did not made it by their own. ''' import sys import urllib2 def download_and_replace(url, target_file): ''' Downloads file through http with progress report. Version by PabloG obtained in stack overflow http://stackoverflow.com/questions/22676/how-do-i-download-a-file-over-http -using-python ''' # Try to connect to the internet try: u = urllib2.urlopen(url) except Exception, err: if getattr(err, 'code', None): print "\nError: %s Could not get file %s\n" % (err.code, url) else: # A generic error is most possibly no available internet print "\nCould not connect to the internet\n" exit(1) with open(target_file, 'wb') as f: meta = u.info() file_size = int(meta.getheaders("Content-Length")[0]) file_size_dl = 0 block_sz = 8192 while True: buffer = u.read(block_sz) if not buffer: break file_size_dl += len(buffer) f.write(buffer) status = r"%10d [%3.2f%%]" % (file_size_dl, file_size_dl*100./file_size) status = status + chr(8)*(len(status)+1) # CONFIGURATION master_URL = 'https://github.com/LxMLS/lxmls-toolkit/raw/master/' labs_URL = 'https://github.com/LxMLS/lxmls-toolkit/raw/student/' # FILES TO BE REPLACED FOR THAT DAY code_day = { 'day1': ['lxmls/classifiers/multinomial_naive_bayes.py', 'lxmls/classifiers/perceptron.py'], 'day2': ['lxmls/sequences/hmm.py', 'lxmls/sequences/sequence_classification_decoder.py'], 'day3': ['lxmls/sequences/structured_perceptron.py'], 'day4': ['lxmls/parsing/dependency_decoder.py'], 'day5': ['lxmls/deep_learning/mlp.py'], 'day6': ['lxmls/deep_learning/rnn.py'] } # ARGUMENT PROCESSING if ((len(sys.argv) == 2) and (sys.argv[1] in ['day0', 'day1', 'day2', 'day3', 'day4', 'day5', 'day6'])): undo_flag = 0 day = sys.argv[1] elif ((len(sys.argv) == 3) and (sys.argv[1] == '--undo') and (sys.argv[2] in ['day0', 'day1', 'day2', 'day3', 'day4', 'day5', 'day6'])): undo_flag = 1 day = sys.argv[2] else: print ("\nUsage:\n" "\n" "python solve.py day<day number> # To solve exercise \n" "\n" "python solve.py --undo day<day number> # To undo solve\n" "" ) exit(1) # CHECK THERE ARE FILES TO SAVE if day in code_day: print "\nsolving %s" % day else: print "\nTheres actually no code to solve on %s!\n" % day exit() # OVERWRITE THE FILES TO SOLVE THEM for pyfile in code_day[day]: if undo_flag: download_and_replace(labs_URL + pyfile, pyfile) print "Unsolving: %s" % pyfile else: download_and_replace(master_URL + pyfile, pyfile) print "Solving: %s" % pyfile
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"""Module of app configuration""" import os basedir = os.path.abspath(os.path.dirname(__file__)) class Config: """Class of configuration""" # Form SECRET_KEY = os.environ.get('SECRET_KEY') or \ b'\x876\xeb_\xc9<?\xb8r\xcak\r[\xa0\xf4\xfe\xdbP\xae\x17\x15S\xa5^' # Mail MAIL_SERVER = os.environ.get('MAIL_SERVER', 'smtp.gmail.com') MAIL_PORT = int(os.environ.get('MAIL_PORT', '587')) MAIL_USE_TLS = os.environ.get('MAIL_USE_TLS', 'true').lower() in ['true', 'on', '1'] MAIL_USERNAME = os.environ.get('MAIL_USERNAME') MAIL_PASSWORD = os.environ.get('MAIL_PASSWORD') FEEDBACK_FORUM_MAIL_SUBJECT_PREFIX = '[Feedback Forum]' FEEDBACK_FORUM_MAIL_SENDER = 'Feedback Forum' # DataBase SQLALCHEMY_TRACK_MODIFICATIONS = False # Administrator ADMIN_NAME = os.environ.get('ADMIN_NAME') ADMIN_PASSWORD = os.environ.get('ADMIN_PASSWORD') # Review Statuses REVIEW_STATUSES = [ 'PENDING', 'PROCESSING', 'CLOSED', ] @staticmethod def init_app(app): """Initialize the app with this configuration""" class DevelopmentConfig(Config): """Class of configuration on developing""" DEBUG = True SQLALCHEMY_DATABASE_URI = os.environ.get('DEV_DATABASE_URL') or \ 'sqlite:///' + os.path.join(basedir, 'data-dev.sqlite') class TestingConfig(Config): """Class of configuration on testing""" TESTING = True SQLALCHEMY_DATABASE_URI = os.environ.get('TEST_DATABASE_URL') or \ 'sqlite://' WTF_CSRF_ENABLED = False class ProductionConfig(Config): """Class of configuration on production""" SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL') or \ 'sqlite:///' + os.path.join(basedir, 'data.sqlite') config = { 'development': DevelopmentConfig, 'testing': TestingConfig, 'production': ProductionConfig, 'default': DevelopmentConfig }
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# coding: utf8 import sys from setuptools import find_packages, setup from setuptools.command.test import test as TestCommand setup( name="dogerpc", version="0.1.4", description="A RPC Framework", long_description=open("README.md").read(), long_description_content_type="text/markdown", author="Timmy", author_email="[email protected]", url="http://github.com/zhu327/doge", packages=["doge"] + [f"{'doge'}.{i}" for i in find_packages("doge")], license="Apache License 2.0", keywords=["rpc", "etcd", "messagepack", "gevent", "microservices"], classifiers=[ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "License :: OSI Approved :: Apache Software License", "Programming Language :: Python", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", ], install_requires=["mprpc", "pyformance", "python-etcd",], tests_require=["pytest",], cmdclass={"test": PyTest}, )
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2.607748
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""" Adaptor for reading and writing any generic text file. This is a good example of a very simple adaptor class. """ from .adaptor import Adaptor, SleapObjectType from .filehandle import FileHandle
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3.811321
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#rearrangeNumber(kg, s, v) # # #(kg, s, v) = extractNumber('ref.txt') #(kgs_c, kgr_c, ss_c, sr_c, vs_c, vr_c) = rearrangeNumber(kg, s, v) #kg_matrix = addToMatrix(kg_matrix, kgs_c, kgr_c, 0) #s_matrix = addToMatrix(s_matrix, ss_c, sr_c, 0) #v_matrix = addToMatrix(v_matrix, vs_c, vr_c, 0) # #(kg, s, v) = extractNumber('refx4.txt') #(kgs_c, kgr_c, ss_c, sr_c, vs_c, vr_c) = rearrangeNumber(kg, s, v) #kg_matrix = addToMatrix(kg_matrix, kgs_c, kgr_c, 1) #s_matrix = addToMatrix(s_matrix, ss_c, sr_c, 1) #v_matrix = addToMatrix(v_matrix, vs_c, vr_c, 1) # #(kg, s, v) = extractNumber('transpose2.txt') #(kgs_c, kgr_c, ss_c, sr_c, vs_c, vr_c) = rearrangeNumber(kg, s, v) #kg_matrix = addToMatrix(kg_matrix, kgs_c, kgr_c, 2) #s_matrix = addToMatrix(s_matrix, ss_c, sr_c, 2) #v_matrix = addToMatrix(v_matrix, vs_c, vr_c, 2) # #for m in kg_matrix: # print(m) #for m in s_matrix: # print(m) #for m in v_matrix: # print(m) if __name__ == "__main__": main()
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1.750809
618
#!/usr/bin/env python import load from gna.bundle import execute_bundle from gna.configurator import NestedDict, uncertaindict, uncertain from gna.env import env # # Bundle configuration # cfg = NestedDict( bundle = dict( name='parameters', version='ex01', ), pars = uncertaindict( [ ( 'par_a', (1.0, 1.0, 'percent') ), ( 'par_b', (2.0, 0.01, 'relative') ), ( 'par_c', (3.0, 0.5, 'absolute') ), ( 'group.a', (1.0, 'free' ) ), ( 'group.b', (1.0, 'fixed', 'Labeled fixed parameter' ) ) ], ), ) # # Execute bundle configuration # b1 = execute_bundle(cfg) # # Print the parameters # env.globalns.printparameters(labels=True)
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2.07438
363
from django.conf.urls import url from django.contrib import admin from message import views # template tagging for relative url app_name = 'message' urlpatterns = [ url(r'^$', views.home, name='home'), url(r'^inbox$', views.inbox, name='inbox'), url(r'^outbox$', views.outbox, name='outbox'), url(r'^compose$', views.compose, name='compose'), ]
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2.654412
136
# Copyright (C) 2022 Intel Corporation # SPDX-License-Identifier: Apache-2.0 # from mmcls.datasets.builder import DATASETS from .multi_cls_dataset import MultiClsDataset from .cls_csv_dataset import CSVDatasetCls from mpa.modules.utils.task_adapt import map_class_names import numpy as np @DATASETS.register_module() @DATASETS.register_module()
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2.734375
128
# Should be smallest now n=input print("IO hb,e cmoym ek etyhbeo agrudy!. "[int(n())>len(set(n().split()[1:]+n().split()[1:]))::2])
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2.095238
63
# Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys #import sphinx_rtd_theme import sphinx_bootstrap_theme import subprocess import pathlib from pathlib import Path generate_doxygen() # -- Project information ----------------------------------------------------- project = 'Hypervisor Memory Introspection' copyright = '2020, Bitdefender' author = 'Bitdefender' # The major project version, used as the replacement for |version|. version = "1" # The full project version, used as the replacement for |release| and e.g. in the HTML templates. release = '1.132.1' # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.todo', 'sphinx.ext.autosectionlabel', 'sphinx_bootstrap_theme' ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # Tell sphinx what the primary language being documented is. primary_domain = 'c' # Tell sphinx what the pygments highlight language should be. highlight_language = 'c' todo_include_todos = False # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'chapters/global-options.rst', 'chapters/process-options.rst'] # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'bootstrap' html_logo = 'chapters/images/hvmi-logo-main-color.png' html_use_index = True if html_theme == 'bootstrap': html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() html_theme_options = { 'bootstrap_version': "3", 'navbar_site_name': 'Chapters', 'navbar_links': [ ("GitHub", "https://github.com/hvmi/hvmi", True), ("Blog", "https://hvmi.github.io/blog/", True), ("Doxygen", "_static/doxygen/html/index"), ], 'source_link_position': "footer", } # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] master_doc = 'index' # autosectionlabel settings # True to prefix each section label with the name of the document it is in, followed by a colon. autosectionlabel_prefix_document = True # Uncomment this to use custom.css
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3.284855
997
from sevenbridges.meta.fields import StringField from sevenbridges.meta.resource import Resource class VolumeFile(Resource): """ VolumeFile resource describes the location of the file on the external volume. """ volume = StringField(read_only=True) location = StringField(read_only=True)
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3.376344
93
from common.webdriver_factory import get_driver from selenium.webdriver.support.wait import WebDriverWait from selenium.webdriver.support import expected_conditions as EC from selenium.webdriver.common.by import By driver = get_driver('chrome') wait = WebDriverWait(driver, 5) driver.get('https://www.mlb.com/es/standings') driver.quit()
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3.238095
105
from core.modules import BaseClass
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4.5
8
# Generated by Django 2.1.1 on 2018-10-09 01:31 from django.db import migrations, models
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2.84375
32
"""Pass."""
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2.4
5
import numpy as np from gym.spaces import Box from metaworld.envs import reward_utils from metaworld.envs.asset_path_utils import full_v2_path_for from metaworld.envs.mujoco.sawyer_xyz.sawyer_xyz_env import SawyerXYZEnv, _assert_task_is_set
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2.641304
92
from metarl.envs import MetaRLEnv from metarl.experiment import LocalTFRunner from metarl.np.algos import CMAES from metarl.np.baselines import LinearFeatureBaseline from metarl.sampler import OnPolicyVectorizedSampler from metarl.tf.policies import CategoricalMLPPolicy from tests.fixtures import snapshot_config, TfGraphTestCase
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3.42268
97
import testutils import json import psycopg2
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3.428571
14
# -*- coding: utf-8 -*- from __future__ import print_function, division, absolute_import import unittest from flypy import jit, ijit #===------------------------------------------------------------------=== # Tests #===------------------------------------------------------------------=== if __name__ == '__main__': unittest.main()
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4.084337
83
# Copyright 2021 Google LLC # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """Test suite for Switchboard capability.""" import os.path import time from typing import Tuple, Type from gazoo_device.switchboard import log_process from gazoo_device.tests.functional_tests.utils import gdm_test_base class SwitchboardTestSuite(gdm_test_base.GDMTestBase): """Test suite for Switchboard capability.""" @classmethod def is_applicable_to(cls, device_type: str, device_class: Type[gdm_test_base.DeviceType], device_name: str) -> bool: """Determine if this test suite can run on the given device.""" return device_class.has_capabilities(["switchboard"]) @classmethod def requires_pairing(cls) -> bool: """Returns True if the device must be paired to run this test suite.""" return False @classmethod def required_test_config_variables(cls) -> Tuple[str, ...]: """Returns keys required to be present in the functional test config.""" return ("shell_cmd", "expect") def test_send_and_expect(self): """Tests send_and_expect() method.""" timeout = 10 # In seconds. response = self.device.switchboard.send_and_expect( self.test_config["shell_cmd"], self.test_config["expect"], timeout=timeout) self.assertFalse( response.timedout, "{} switchboard.send_and_expect failed for command {!r}. " "Did not find regex {!r} in {}s. Device output: {!r}" .format(self.device.name, self.test_config["shell_cmd"], self.test_config["expect"], timeout, response.before)) def test_do_and_expect(self): """Tests switchboard.do_and_expect() method.""" switch = MockPowerSwitch() expect_result = self.device.switchboard.do_and_expect( switch.turn_on_power, (), {}, ["fake_string, won't match anything"], timeout=.1) self.assertTrue( expect_result.timedout, "Expected do_and_expect to time out, but timedout was False") self.assertTrue(switch.power_is_on, "switch.turn_on_power() did not execute. " "The power state is still off for switch.") def test_expect_with_bogus_logline(self): """Tests switchboard.expect() method for a log line that doesn't exist.""" phrase = "garblygookand more" response = self.device.switchboard.expect([phrase], timeout=2) self.assertTrue(response.timedout, "Response should have timed out, but it didn't. " f"Requested log line regex: {phrase!r}. " f"Device output: {response.before!r}") def test_rotate_log(self): """Tests max_log_size and auto log rotation features.""" old_log_file_name = self.device.log_file_name expected_log_filename = log_process.get_next_log_filename(old_log_file_name) expected_message = "Special message to trigger at least one log rotation" max_log_size = len(expected_message) * 10 self.device.switchboard.set_max_log_size(max_log_size) time.sleep(.5) # Allow time for set_max_log_size to complete. try: for _ in range(20): self.device.switchboard.add_log_note(expected_message) end_time = time.time() + 3 while (old_log_file_name == self.device.log_file_name and time.time() < end_time): time.sleep(0.1) self.assertTrue( os.path.exists(old_log_file_name), f"Expected old log file name {old_log_file_name} to exist") self.assertTrue( os.path.exists(expected_log_filename), f"Expected new log file name {expected_log_filename} to exist") self.assertNotEqual( old_log_file_name, self.device.log_file_name, f"Expected log file name to change from {old_log_file_name}") finally: # Disable log rotation (the default) after the test. self.device.switchboard.set_max_log_size(0) if __name__ == "__main__": gdm_test_base.main()
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2.585155
1,738
from helpfuncs import bitdecoding # initialize and fill list for set based on base relations bsplit = [(len(bitdecoding(i+1)),bitdecoding(i+1)) for i in xrange(255)]
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3.111111
54
SECRET_KEY = "changeme please"
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2.583333
12
from server.controller.controllers import RobotController, TextRobot
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4.4375
16
mystring = mystring.expandtabs()
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2.75
12
from app import app from app import controller from flask import request control = controller.Controller() @app.route('/api/login', methods=['POST']) @app.route('/api/logout') @app.route('/mailboxes') @app.route('/search_emails') @app.route('/emails') @app.route('/email')
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2.89899
99
# Generated by Django 3.2.3 on 2021-05-14 07:39 from django.db import migrations
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2.766667
30
""" gathering of blocks/group of layers used in domainnet. author: David-Alexandre Beaupre date: 2020-04-27 """ import torch import torch.nn as nn import torch.nn.functional as F
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3.172414
58
from os.path import split, join, abspath, exists from os import environ class PathHelper: """This class provides a set of assisting functions to deal with path issues.""" @classmethod def abspath_of_executable(cls, path: str): """Given a command that can run in shell (with the current environment settings), this function figures out the absolute path to the command. e.g.:: python3 -> /usr/bin/python3 if the given path does not target to any file, it will raise an FileNotFound exception. :raises FileNotFoundError: no executable can be found at `path` :rtype: str """ base_path, name = split(path) if base_path == '': # this is the name of a program # search from PATH if 'PATH' not in environ: raise FileNotFoundError else: for prefix in environ['PATH'].strip().split(':'): prefix = prefix.strip() if exists(join(prefix, name)): return join(prefix, name) raise FileNotFoundError else: full_path = abspath(path) if not exists(full_path): raise FileNotFoundError else: return full_path
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2.20197
609
# Licensed to the Apache Software Foundation (ASF) under one # or more contributor license agreements. See the NOTICE file # distributed with this work for additional information # regarding copyright ownership. The ASF licenses this file # to you under the Apache License, Version 2.0 (the # "License"); you may not use this file except in compliance # with the License. You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, # software distributed under the License is distributed on an # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY # KIND, either express or implied. See the License for the # specific language governing permissions and limitations # under the License. from argparse import ArgumentParser, Namespace def train_parse_args(train: bool) -> Namespace: """ Parse command line arguments. :returns: a namespace with all the set parameters """ parser = ArgumentParser(description="Annotate a sample of the given files in the input directory") parser.add_argument("--model-dir", help="Model directory", action="store", dest="model_dir", required=False) parser.add_argument( "--input-files-dir", help="Input files directory", action="store", dest="input_dir", required=True ) parser.add_argument( "--dev-set-size", help="Size of dev set", action="store", dest="dev_size", type=float, required=False ) parser.add_argument("--nb_segment", help="Number of segment", action="store", type=int, required=False) parser.add_argument("--segment", help="Number of segment", action="store", type=int, required=False) if train: parser.add_argument("--epochs", help="Number of epochs", action="store", type=int, dest="epoch", required=True) return parser.parse_args()
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3.357782
559
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import pytest import os from imagine import imagine
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3.871345
171
import numpy as np import torch
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3.363636
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import re import hashlib import requests import cv2 import numpy as np from bs4 import BeautifulSoup from SunGazer.Collectors.Camera import Cam class GeoVisionCam(Cam): """ GeoVision IP camera class. """ def __init__(self, cam_address): """ Construct a cam object. Parameters ---------- cam_address : str url to the IP camera login page. """ super().__init__() self.cam_address = cam_address self.user_token = None self.pass_token = None self.desc_token = None @staticmethod def login(self, username, pwd): """ Login to the IP camera. Parameters ---------- username : str username for the IP camera. pwd : str password for the IP camera. """ umd5, pmd5 = self._get_hashed_credentials(username, pwd) data = { 'grp': -1, 'username': '', 'password': '', 'Apply': 'Apply', 'umd5': umd5, 'pmd5': pmd5, 'browser': 1, 'is_check_OCX_OK': 0 } headers = { 'User-Agent': 'Mozilla' } c = requests.post('{}/LoginPC.cgi'.format(self.cam_address), data=data, headers=headers) self.user_token, self.pass_token, self.desc_token = re.search( r'gUserName\s=\s\"(.*)\";\n.*\s\"(.*)\";\n.*\"(.*)\"', c.text).groups() def cap_pic(self, output='array'): """ Capture a picture. Parameters ---------- output : str, default 'array' output type of the picture, if a path given, the picture will be saved there. Returns ------- numpy.array image array. """ if self.user_token and self.pass_token and self.desc_token: data = { 'username': self.user_token, 'password': self.pass_token, 'data_type': 0, 'attachment': 1, 'channel': 1, 'secret': 1, 'key': self.desc_token } r = requests.post('{}/PictureCatch.cgi'.format(self.cam_address), data=data, stream=True) if output.lower() == 'array': return cv2.imdecode(np.frombuffer(r.content, np.uint8), -1) # write the image in the disk with open(output, 'wb') as f: for chunk in r.iter_content(): f.write(chunk) else: raise Exception('Authentication failed! Wrong username or password!') def cap_video(self, output): """ Capture video. """ raise NotImplementedError('This method is not implemented yet!')
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from ipywidgets import DOMWidget from traitlets import Unicode, Int
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#!/usr/bin/env python #pythonlib import os import re import sys import math import time import glob import numpy import shutil import subprocess #appion from appionlib import apFile from appionlib import apParam from appionlib import apImage from appionlib import apDisplay from appionlib import apDatabase from appionlib import appiondata from appionlib import appionLoop2 from appionlib import apInstrument from appionlib.apCtf import ctfdb from appionlib.apCtf import ctfinsert # other myami from pyami import mrc, primefactor, imagefun class Ace2Loop(appionLoop2.AppionLoop): """ appion Loop function that runs Craig's ace2 program to estimate the CTF in images """ #====================== #====================== #====================== #====================== #====================== def reprocessImage(self, imgdata): """ Returns True, if an image should be reprocessed False, if an image was processed and should NOT be reprocessed None, if image has not yet been processed e.g. a confidence less than 80% """ if self.params['reprocess'] is None: return True ctfvalue = ctfdb.getBestCtfByResolution(imgdata, msg=False) if ctfvalue is None: return True if conf > self.params['reprocess']: # small, unbinned images can give same defocus values for 1 & 2: if self.params['bin'] == 1 or ctfvalue['defocus1'] != ctfvalue['defocus2']: return False return True #====================== #====================== #====================== #====================== #====================== if __name__ == '__main__': imgLoop = Ace2Loop() imgLoop.run()
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#Importing os module and defining application's path import os basedir = os.path.abspath(os.path.dirname(__file__)) DEBUG = True SQLALCHEMY_ECHO = True #Cross-site_request_forgery_(CSRF)_protection_provided_by_WTforms WTF_CSRF_ENABLED = True #The secret key that scrf uses for authentication SECRET_KEY = 'This-must-be-changed' #The path to the database SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.join(basedir, 'barber_shop.db') #By disabling this, we decrease the overload SQLALCHEMY_TRACK_MODIFICATIONS = False # Reference: https://blog.miguelgrinberg.com/post/the-flask-mega-tutorial-part-vii-unit-testing # Mail Server Settings MAIL_SERVER = 'localhost' MAIL_PORT = 25 MAIL_USERNAME = None MAIL_PASSWORD = None
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#coding=utf-8 import logging import hashlib import urlparse import random from django.core.urlresolvers import reverse from django.utils import timezone from django.conf import settings from django.contrib.auth.models import User, Permission from django.db import models from django.utils.translation import ugettext_lazy as _ from biz.account.settings import USER_TYPE_CHOICES, QUOTA_ITEM, NotificationLevel, TimeUnit from biz.account.mixins import LivingDeadModel from biz.idc.models import UserDataCenter LOG = logging.getLogger(__name__) User.profile = property(lambda u: UserProfile.objects.get_or_create(user=u)[0]) NOTIFICATION_KEY_METHODS = ((NotificationLevel.INFO, 'info'), (NotificationLevel.SUCCESS, 'success'), (NotificationLevel.ERROR, 'error'), (NotificationLevel.WARNING, 'warning'), (NotificationLevel.DANGER, 'danger')) # This loop will create some is_xxx(eg, is_info, is_success..) property for value, name in NOTIFICATION_KEY_METHODS: bind(value) # This loop will create some action method, user can create notification like this way: # Notification.info(receiver, title, content) for value, name in NOTIFICATION_KEY_METHODS: bind(value)
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# -*- coding: utf-8 -*- import json import datetime from geoposition import Geoposition from web.processors.event import create_or_update_event
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#coding=utf-8 # # # Copyright (C) 2013 INAF -IRA Italian institute of radioastronomy, [email protected] # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # """ Subscan related classes and funcions: B{Classes} - SubscanError - Subscan: a generic subscan - OTFSubscan: a generic on the fly subscan - SiderealSubscan: a generic sidereal subscan B{Functions} Used to get subscan classes instances. Subscans are often returned in couples together with their associated Tsys sidereal subscan. - get_cen_otf_subscan - get_ss_otf_subscan (not implemented) - get_sidereal_subscan - get_tsys_subscan - get_couple_subscan - get_sid_couple_subscan """ from past.builtins import cmp from builtins import str import logging logger = logging.getLogger(__name__) import copy from persistent import Persistent from ..valid_angles import VAngle from .. import templates, frame, utils, procedures from ..errors import ScheduleError, ScanError from ..frame import NULL_COORD, Coord, EQ, GAL, HOR, NULL TSYS_SIGMA = 5 """ Used for calculating TSYS subscans coordinate offsets as TSYS_SIGMA * beamsize """ class Subscan(Persistent): """ Generic subscan. Contains common subscan attributes and is meant to be override by specific subscan classes """ ID = 1 #static counter attribute def __init__(self, _target, duration=0.0, is_tsys=False, is_cal=False): """ Constructor. Give the subscan a unique ID. """ self.ID = Subscan.ID #This value will be the same found in the lis file Subscan.ID += 1 self.target = _target self.is_tsys = is_tsys self.duration = duration #self.SEQ_ID = 0 #position in the respective scan, default value 0 self.is_cal = is_cal if self.is_cal and self.is_tsys: raise ScheduleError("Subscan cannot be tsys and cal at the same time") if self.is_cal: self.pre_procedure = procedures.CALON self.post_procedure = procedures.CALOFF elif self.is_tsys: self.pre_procedure = procedures.NULL self.post_procedure = procedures.TSYS else: #Default self.pre_procedure = procedures.NULL self.post_procedure = procedures.NULL class OTFSubscan(Subscan): """ On the flight sunbscan class """ def __init__(self, _target, lon2, lat2, descr, scan_frame, geom, direction, duration, is_tsys=False, is_cal=False): """ Constructor. @type lon2: VAngle @type lat2: VAngle """ Subscan.__init__(self, _target, duration, is_tsys, is_cal) self.typename = "OTF" self.scan_frame = scan_frame #check that offset frame and scan frame are equal if self.target.offset_coord.frame == frame.NULL:#default behaviour self.target.offset_coord.frame = self.scan_frame if not self.target.offset_coord.frame == self.scan_frame: msg = "offset frame %s different from scan frame %s" % (self.target.offset_coord.frame.name, self.scan_frame) logger.debug(msg) raise ScheduleError(msg) self.lon2 = lon2 self.lat2 = lat2 self.descr = descr.upper() #check consistnecy of frames specifications #we already know that offset and scan if not self.target.coord.frame == self.scan_frame:#possible mistake! logger.warning("SUBSCAN %d : scan_frame and coordinates_frame are different" % (self.ID,)) if (self.target.coord.frame == frame.EQ and self.descr == "CEN" and self.scan_frame == frame.HOR): pass #OK - only success condition else: raise ScheduleError("not compatible frame types")#very bad! self.geom = geom self.direction = direction def get_cen_otf(_target, duration, length, offset, const_axis, direction, scan_frame): """ Get an I{OTF} subscan with description I{CEN}. @type length: VAngle @type offset: VAngle @return: an L{OTFSubscan} instance """ __target = copy.deepcopy(_target) if const_axis == "LON": __target.offset_coord.lon = _target.offset_coord.lon + offset logger.debug("offset lon: %f" % (__target.offset_coord.lon.deg,)) lon2 = VAngle(0.0) lat2 = length elif const_axis == "LAT": __target.offset_coord.lat = _target.offset_coord.lat + offset logger.debug("offset lat: %f" % (__target.offset_coord.lat.deg,)) lon2 = length lat2 = VAngle(0.0) attr = dict(_target = __target, descr = 'CEN', duration = duration, lon2 = lon2, lat2 = lat2, geom = const_axis, direction = direction, scan_frame = scan_frame, ) return OTFSubscan(**attr) def get_ss_otf(*args, **kwargs): """ @raise NotImplementedError: we still have no useful case for implemting this function """ raise NotImplementedError("is there any useful case for implementing this?") def get_sidereal(_target, offset=NULL_COORD, duration=0.0, is_tsys=False, is_cal=False): """ @param _target: the subscan target @type _target: target.Target @param offset_lon: additional longitude offset @type offset_lon: VAngle @param offset_lat: additional latitude offset @type offset_lat: VAngle """ __target = copy.deepcopy(_target) #import ipdb;ipdb.set_trace() __target.offset_coord += offset return SiderealSubscan(__target, duration, is_tsys, is_cal) def get_tsys(_target, offset, duration=0.0): """ Get a Tsys subscan. This basically returns a SIDEREAL subscan where source name is I{Tsys} and duration is I{0.0} @type offset_lon: VAngle @type offset_lat: VAngle """ __target = copy.deepcopy(_target) __target.label = "Tsys" st = get_sidereal(__target, offset, duration=0.0, is_tsys=True) st.post_procedure = procedures.TSYS return st def get_cen_otf_tsys(_target, duration, length, offset, const_axis, direction, scan_frame, beamsize): """ Get a couple composed of a CEN_OTF subscan and its relative SIDEREAL TSYS subscan. @return: (otf_subscan, tsys_subscan) @type length: VAngle @type offset: Coord @type beamsize: VAngle """ logger.debug("get couple subscan offset: %s " % (offset,)) negative_offset = VAngle(-1 * (length.deg / 2.0 + beamsize.deg * TSYS_SIGMA)) positive_offset = VAngle(length.deg / 2.0 + beamsize.deg * TSYS_SIGMA) if const_axis == "LAT": _offset_lat = offset if direction == "INC": _offset_lon = negative_offset elif direction == "DEC": _offset_lon = positive_offset elif const_axis == "LON": _offset_lon = offset if direction == "INC": _offset_lat = negative_offset elif direction == "DEC": _offset_lat = positive_offset _offset = Coord(scan_frame, _offset_lon, _offset_lat) ss = get_cen_otf(_target, duration, length, offset, const_axis, direction, scan_frame) st = get_tsys(_target, _offset) return ss, st def get_sid_tsys(_target, offset, extremes, duration, beamsize): """ Get a couple of sidereal subscans, where the first is an actual subscan and the second is a tsys subscan obtained pointing the antenna out of a rectangular polygon containing the source. @param _target: the source to be observed @type _target: L{target.Target} @param offset_lon: longitude offset of the subscan @type offset_lon: VAngle @param offset_lat: latitude offset of the subscan @type offset_lat: VAngle @param extremes: An array containing the offsets of the extremes of the rectangular polygon containing the source (i.e. the borders of a raster map) @type extremes: [(x0,y0), (x1,y1), (x2,y2), (x3,y3)] @param duration: subscan duration (Sec. ) @type duration: float @param beamsize: beam size used to calculated tsys subscan offsets @type beamsize: VAngle """ ss = get_sidereal(_target, offset, duration) tsys_offsets = utils.extrude_from_rectangle(offset.lon.deg, offset.lat.deg, extremes, beamsize.deg * TSYS_SIGMA) _offsets = Coord(offset.frame, VAngle(tsys_offsets[0]), VAngle(tsys_offsets[1])) st = get_tsys(_target, _offsets) return ss, st
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2.270921
4,278
#!/usr/bin/env python # -*- coding: utf-8 -*- ''' ## © Copyright (C) 2016-2020 Xilinx, Inc ## ## Licensed under the Apache License, Version 2.0 (the "License"). You may ## not use this file except in compliance with the License. A copy of the ## License is located at ## ## http://www.apache.org/licenses/LICENSE-2.0 ## ## Unless required by applicable law or agreed to in writing, software ## distributed under the License is distributed on an "AS IS" BASIS, WITHOUT ## WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the ## License for the specific language governing permissions and limitations ## under the License. ''' ################################################################## # Evaluation of frozen/quantized graph ################################################################# ''' TESTED WITH PYTHON 3.6 Author: Mark Harvey ([email protected]) Date: 28 May 2019 Modified by Daniele Bagni ([email protected]) Date: 27 Aug 2019 ''' import os import sys import glob import argparse import shutil import tensorflow as tf import numpy as np import cv2 import gc # memory garbage collector #DB import tensorflow.contrib.decent_q from tensorflow.python.platform import gfile from config import fashion_mnist_config as cfg #DB #DB DATAS_DIR = cfg.DATASET_DIR TEST_DIR = os.path.join(DATAS_DIR, "test") print("\n eval_graph.py runs from ", DATAS_DIR) if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('--graph', type=str, default='./freeze/frozen_graph.pb', help='graph file (.pb) to be evaluated.') parser.add_argument('--input_node', type=str, default='images_in', help='input node.') parser.add_argument('--output_node', type=str, default='dense_1/BiasAdd', help='output node.') parser.add_argument('--class_num', type=int, default=cfg.NUM_CLASSES, help='number of classes.') parser.add_argument('--gpu', type=str, default='0', help='gpu device id.') FLAGS, unparsed = parser.parse_known_args() tf.app.run(main=main, argv=[sys.argv[0]] + unparsed)
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2.521173
921
import os from yattag import Doc, indent from libs.utils import create_stamped_temp, slugify import matplotlib.pyplot as plt # NOTE - Does not work out of the box, needs a fix: # # Annoyingly, the js loading of subpages violates Cross-Origin Requests policy in all browsers # when files are served locally via file:///. Works fine for http protocol though. # It is possible to use iframes rather than js loader, but it's ugly and has other issues (multiple nested scrollbars). # # Workarounds: # - Firefox: # - go to about:config -> search for privacy.file_unique_origin and toggle # - then set up Firefox as the default for opening .htm files (that's the reason why I do not use .html) # - Chrome # - can be started with "--allow-file-access-from-files", then it should just work # - it would be possible to start the appropriate process in .show, but I have not tried # - one workaround is enough for me # - https://stackoverflow.com/a/18137280 # - Edge: # - until recently, it was the only browser not enforcing the CORS policy for local files, so it just # worked. The new version of Edge enforces the same, do not know how to get around there. # - or it is possible to use local webserver and serve the files via it # - CORS policy is respected with http # - python webserver works fine, just serving the directory: python -m http.server 8000 # - however seems more hassle than just changing firefox config... # I am not using it at the end, not sure if it works correctly.
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3.092664
518
version = '2.3.1' version_cmd = 'elasticsearch -version' download_url = 'http://packages.elasticsearch.org/GPG-KEY-elasticsearch' install_script = """ apt-key add GPG-KEY-elasticsearch echo "deb http://packages.elasticsearch.org/elasticsearch/VERSION/debian stable main" > /etc/apt/sources.list.d/elasticsearch.list apt-get update -qq apt-get install -y elasticsearch service elasticsearch start """
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3.053435
131
# Converts a 'str.out' file to the VASP POSCAR format. # # Assumes: # + You have installed the "ase" python package. # + You have the "str2cif" tool from ATAT in your path. # # Author: Jesper Kristensen import os, sys from ase import io #=== USER SETTINGS: structure_from = 'str.out' structure_to = 'str.POSCAR' if not os.path.exists(structure_from): print 'EEEE ATAT file %s does not exist in the path!' print 'EEEE You have to specify the ATAT file in this Python script.' print 'EEEE exiting ...' sys.exit(1) #=== Convert str.out to CIF format first: print print 'IIII Converting ATAT to CIF format ...' tmp = 'tmp.cif' cmd = 'str2cif < %s > %s' % (structure_from, tmp) os.system(cmd) #=== Then convert CIF to POSCAR using ASE: print 'IIII Converting CIF to POSCAR format ...' atoms = io.read(tmp) atoms.write(structure_to, format = 'vasp') #=== Clean up: os.remove(tmp) print 'IIII All done, the resulting POSCAR file is in %s' % structure_to print
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2.666667
372
import logging from iribaker import to_iri from rdflib import URIRef, Literal, Namespace from representation import Predicate, Entity, Triple, Provenance logger = logging.getLogger(__name__)
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3.305085
59
from .platform import OS from .windows.win import winPass from .linUni.linUni import linUniPass from .manager import Manager import inquirer if __name__ == "__main__": main()
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3.05
60
import os from logging import Logger from typing import Dict, Optional from src.app.io import (get_checkpoints_dir, get_train_log_file, get_train_logs_dir, load_trainset, load_valset, save_prep_name, save_testset, save_trainset, save_valset) from src.app.pre.prepare import get_prepared_dir, load_filelist from src.app.utils import prepare_logger from src.app.waveglow.io import get_train_dir from src.core.common.train import get_custom_or_last_checkpoint from src.core.pre.merge_ds import split_prepared_data_train_test_val from src.core.waveglow.model_checkpoint import CheckpointWaveglow from src.core.waveglow.train import continue_train, train if __name__ == "__main__": mode = 0 if mode == 0: start_new_training( base_dir="/datasets/models/taco2pt_v5", train_name="debug", prep_name="thchs_ljs", custom_hparams={ "batch_size": 3, "iters_per_checkpoint": 5, "cache_wavs": False }, validation_size=0.001, ) elif mode == 1: continue_training( base_dir="/datasets/models/taco2pt_v5", train_name="debug" )
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2.266795
521
"""Template class.""" import os # For Mypy typing from typing import Any # noqa pylint: disable=unused-import from typing import Dict # noqa pylint: disable=unused-import import jinja2 class Template(object): # pylint: disable=too-few-public-methods """Represents tepmplate which can be rendered.""" def __init__(self, file_path, context): # type: (str, Dict[str, Any]) -> None """Constructor.""" self.file_path = file_path # type: str self.context = context # type: Dict[str, Any] def render(self): # type () -> str """Render template.""" if not os.path.exists(self.file_path): import hardest.exceptions message = ('Path "{}" not exists.' .format(self.file_path)) raise hardest.exceptions.TemplateNotFoundException(message) file_handler = open(self.file_path) template_content = str(file_handler.read()) file_handler.close() template = jinja2.Template(template_content) rendered_content = str(template.render(**self.context)) return rendered_content
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2.454741
464
import datetime from django.shortcuts import render from django.http import HttpResponse from django.db.models import F from django.conf import settings from models import Counter
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3.8125
48
""" Polarisation animation... the animate_vectors() method creates an interactive 3D plot, visualising the resultant polarisation for a given input of Ex, Ey and the phase difference (in radians) between them Last updated 2018-02-19 JK """ # py 2.7 compatibility from __future__ import (division, print_function, absolute_import) import numpy as np import matplotlib.pyplot as plt import mpl_toolkits.mplot3d.axes3d as p3 import matplotlib.animation as animation #replace default matplotlib text and color sequence with durham colours plt.rc('font',**{'family':'Serif','serif':['Times New Roman']}) params={'axes.labelsize':13,'xtick.labelsize':12,'ytick.labelsize':12,'legend.fontsize': 11,'mathtext.fontset':'cm','mathtext.rm':'serif'} plt.rcParams.update(params) if __name__ == '__main__': animate_vectors(1,1.j,0)
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3
275
# Generated by Django 3.1.7 on 2021-08-10 17:14 from django.db import migrations, models import django.db.models.deletion
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2.818182
44
import logging import torch import torch.nn as nn import torchtext import os from torch.autograd import Variable from tqdm import tqdm from tensorboardX import SummaryWriter from typing import List from framenet_tools.config import ConfigManager
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3.676471
68
#!/usr/bin/env python # Ymake MatrixNet support import sys import os import shutil import re import subprocess if __name__ == '__main__': if len(sys.argv) < 2: print >>sys.stderr, "Usage: build_mn.py <funcName> <args...>" sys.exit(1) if (sys.argv[2:]): globals()[sys.argv[1]](sys.argv[2:]) else: globals()[sys.argv[1]]()
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2.1
180
# Generated by Django 3.2.9 on 2022-01-20 19:34 from django.conf import settings import django.core.validators from django.db import migrations, models import django.db.models.deletion import uuid
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3.061538
65
if __name__=='__main__': n,m = map(int,input().split()) arr = list(map(int,input().split())) brr = list(map(int,input().split())) count = 0 for i in range(max(arr),min(brr)+1): flag = True for j in arr: if i%j!=0: flag = False break if flag: for k in brr: if k%i!=0: flag = False break if flag: count+=1 print(count)
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1.658863
299
# -*- coding: utf-8 -*- """ jes.bridge.terpcontrol ====================== This interacts with the interpreter, to keep the GUI locked down while the interpreter runs. (In JES, "terp" is short for "interpreter," not "terrapin.") :copyright: (C) 2014 Matthew Frazier and Mark Guzdial :license: GNU GPL v2 or later, see jes/help/JESCopyright.txt for details """ import Stoppable import StoppableInput import StoppableOutput from jes.gui.commandwindow.redirect import RedirectStdio from jes.gui.components.threading import threadsafe
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3.262195
164
"""Creating/edition of ICUs.""" from absl import logging import io import json import tornado.web from icubam.backoffice.handlers import base from icubam.db import synchronizer from typing import Dict, Callable
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3.55
60
from django.conf import settings USERPROFILE_SETTINGS = { 'app_verbose_name': "Custom User", 'register_proxy_auth_group_model': True, } if hasattr(settings, 'USERPROFILE'): USERPROFILE_SETTINGS.update(settings.USERPROFILE)
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2.662921
89
import random with open('09.loc', 'w') as f: for i in range(1, 1001): s = str(i) + ' ' + str(random.randint(1, 100)) + '\n' f.write(s)
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1.962025
79
import scipy.signal as signal import numpy as np
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2.5
22
# Generated by Django 2.1 on 2018-08-27 07:36 from django.db import migrations, models import django.db.models.deletion
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2.904762
42
### # Copyright (c) 2019-2020 Micro Focus or one of its affiliates. # # Licensed under the MIT License (the "License"); you may not use this file # except in compliance with the License. # # The only warranties for products and services of Micro Focus and its affiliates # and licensors ("Micro Focus") are as may be set forth in the express warranty # statements accompanying such products and services. Nothing herein should be # construed as constituting an additional warranty. Micro Focus shall not be # liable for technical or editorial errors or omissions contained herein. The # information contained herein is subject to change without notice. ### """ base helper functions for helm scripts """ import subprocess
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4.641026
156
from conans import ConanFile, CMake, tools import os
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3.6
15
import platform if platform.python_version() < '2.7': unittest = __import__('unittest2') else: import unittest from . import SKIP_BTYPES from riak.bucket import RiakBucket, BucketType from riak import RiakError, RiakObject
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2.752941
85
import sys import csv import scraper if __name__ == "__main__": source_filename = sys.argv[1] destination_filename = sys.argv[2] word_column = int(sys.argv[3]) definition_column = int(sys.argv[4]) with open(source_filename, "r") as source_file: with open(destination_filename, "w") as destination_file: source = csv.reader(source_file, delimiter="\t") destination = csv.writer(destination_file, delimiter="\t") for row in source: row[definition_column] = scraper.generate_definition(row[word_column]) print(row[word_column]) destination.writerow(row)
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2.289655
290
from flask import render_template from . import arturo @arturo.route('/es/machine-learning', methods=['GET']) @arturo.route('/machine-learning', methods=['GET']) @arturo.route('/en/machine-learning', methods=['GET'])
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3.041667
72
from cog.torque import Graph import unittest import os import shutil DIR_NAME = "TorqueTest4" if __name__ == '__main__': unittest.main()
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2.636364
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import sys print(sys.argv[0])
[ 11748, 25064, 628, 198, 4798, 7, 17597, 13, 853, 85, 58, 15, 12962, 198 ]
2.285714
14
from plugins import BasePlugin from plugins import PluginsData from etllib.conf import Conf from etllib.csv import CSV import os
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3.232558
43
from django.urls import path from django.conf.urls import url from django.views import generic from .views import ( BookListView, BookDetailView, BookUpdateView, delete_book, user_booklist, user_booklist_update, BookCreateView, ReviewCreateView, review_update_view ) app_name = 'books' urlpatterns = [ url(r'^$', BookListView.as_view(), name='books'), url(r'^create/$', BookCreateView.as_view(), name='create'), url(r'^review-create/$', ReviewCreateView.as_view(), name='review_create'), url(r'^(?P<slug>[\w-]+)/review-update/$', review_update_view, name='review_update'), url(r'^recommendations/$', generic.TemplateView.as_view(template_name='books/recommendation.html'), name='recommendation'), url(r'^(?P<slug>[\w-]+)/detail/$', BookDetailView.as_view(), name='detail'), url(r'^(?P<slug>[\w-]+)/update/$', BookUpdateView.as_view(), name='update'), url(r'^(?P<slug>[\w-]+)/delete/$', delete_book, name='delete'), url(r'^user-booklist/$', user_booklist, name='user_booklist'), url(r'^user/booklist/update/$', user_booklist_update, name='user_booklist_update'), ]
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2.629717
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#!/usr/bin/env python # -*- coding: utf-8 -*- from collections import defaultdict from datetime import datetime import numpy as np import pandas as pd class Word(object): """ Word definition. """ # Variables of SIR-like model N = "Population" S = "Susceptible" C = "Confirmed" CI = "Infected" F = "Fatal" R = "Recovered" FR = "Fatal or Recovered" V = "Vaccinated" E = "Exposed" W = "Waiting" # Column names DATE = "Date" START = "Start" END = "End" T = "Elapsed" TS = "t" TAU = "tau" COUNTRY = "Country" ISO3 = "ISO3" PROVINCE = "Province" STR_COLUMNS = [DATE, COUNTRY, PROVINCE] COLUMNS = [*STR_COLUMNS, C, CI, F, R] NLOC_COLUMNS = [DATE, C, CI, F, R] VALUE_COLUMNS = [C, CI, F, R] FIG_COLUMNS = [CI, F, R, FR, V, E, W] # Date format: 22Jan2020 etc. DATE_FORMAT = "%d%b%Y" # Separator of country and province SEP = "/" # EDA RATE_COLUMNS = [ "Fatal per Confirmed", "Recovered per Confirmed", "Fatal per (Fatal or Recovered)" ] # Optimization A = "_actual" P = "_predicted" # Phase name SUFFIX_DICT = defaultdict(lambda: "th") SUFFIX_DICT.update({1: "st", 2: "nd", 3: "rd"}) TENSE = "Type" PAST = "Past" FUTURE = "Future" INITIAL = "Initial" ODE = "ODE" RT = "Rt" # Scenario analysis PHASE = "Phase" SERIES = "Scenario" MAIN = "Main" # Flag UNKNOWN = "-" @classmethod def num2str(cls, num): """ Convert numbers to 1st, 2nd etc. @num <int>: number @return <str> """ if not isinstance(num, int): raise TypeError("@num must be an integer.") q, mod = divmod(num, 10) suffix = "th" if q == 1 else cls.SUFFIX_DICT[mod] return f"{num}{suffix}" @staticmethod def negative_exp(x, a, b): """ Negative exponential function f(x)=A exp(-Bx). @x <float>: x values parameters of the function - a <float> - b <float> """ return a * np.exp(-b * x) @classmethod def date_obj(cls, date_str): """ Convert a string to a datetime object. @date_str <str>: date, like 22Jan2020 @return <datetime.datetime> """ obj = datetime.strptime(date_str, cls.DATE_FORMAT) return obj @staticmethod def flatten(nested_list, unique=True): """ Flatten the nested list. @nested_list <list[list[object]]>: nested list @unique <bool>: if True, only unique values will remain @return <list[object]> """ flattened = sum(nested_list, list()) if unique: return list(set(flattened)) return flattened @staticmethod def validate_dataframe(target, name="df", time_index=False, columns=None): """ Validate the dataframe has the columns. @target <pd.DataFrame>: the dataframe to validate @name <str>: argument name of the dataframe @time_index <bool>: if True, the dataframe must has DatetimeIndex @columns <list[str]/None>: the columns the dataframe must have @df <pd.DataFrame>: as-is the target """ df = target.copy() if not isinstance(df, pd.DataFrame): raise TypeError(f"@{name} must be a instance of <pd.DataFrame>.") if time_index and (not isinstance(df.index, pd.DatetimeIndex)): raise TypeError(f"Index of @{name} must be <pd.DatetimeIndex>.") if columns is None: return df if not set(columns).issubset(set(df.columns)): cols_str = ', '.join( [col for col in columns if col not in df.columns] ) raise KeyError(f"@{name} must have {cols_str}, but not included.") return df @staticmethod def validate_natural_int(target, name="number"): """ Validate the natural (non-negative) number. If the value is natural number and the type was float, will be converted to an integer. @target <int/float/str>: value to validate @name <str>: argument name of the value @return <int>: as-is the target """ s = f"@{name} must be a natural number, but {target} was applied" try: number = int(target) except TypeError: raise TypeError(f"{s} and not converted to integer.") if number != target: raise ValueError(f"{s}. |{target} - {number}| > 0") if number < 1: raise ValueError(f"{s}. This value is under 1") return number @staticmethod def validate_subclass(target, parent, name="target"): """ Validate the target is a subclass of the parent class. @target <object>: target to validate @parent <object>: parent class @name <str>: argument name of the target @return <int>: as-is the target """ s = f"@{name} must be an sub class of {type(parent)}, but {type(target)} was applied." if not issubclass(target, parent): raise TypeError(s) return target @staticmethod def validate_instance(target, class_obj, name="target"): """ Validate the target is a instance of the class object. @target <instance>: target to validate @parent <class>: class object @name <str>: argument name of the target @return <instance>: as-is target """ s = f"@{name} must be an instance of {type(class_obj)}, but {type(target)} was applied." if not isinstance(target, class_obj): raise TypeError(s) return target @classmethod def divisors(cls, value): """ Return the list of divisors of the value. @value <int>: target value @return <list[int]>: the list of divisors """ value = cls.validate_natural_int(value) divisors = [ i for i in range(1, value + 1) if value % i == 0 ] return divisors
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import datetime import os import time import timeit import numpy as np import torch as th class Generator(th.nn.Module): """ Generator of the GAN network """ def turn_on_spectral_norm(self): """ private helper for turning on the spectral normalization :return: None (has side effect) """ from torch.nn.utils import spectral_norm if self.spectral_norm_mode is not None: assert self.spectral_norm_mode is False, \ "can't apply spectral_norm. It is already applied" # apply the same to the remaining relevant blocks for module in self.layers: module.conv_1 = spectral_norm(module.conv_1) module.conv_2 = spectral_norm(module.conv_2) # toggle the state variable: self.spectral_norm_mode = True def turn_off_spectral_norm(self): """ private helper for turning off the spectral normalization :return: None (has side effect) """ from torch.nn.utils import remove_spectral_norm if self.spectral_norm_mode is not None: assert self.spectral_norm_mode is True, \ "can't remove spectral_norm. It is not applied" # remove the applied spectral norm for module in self.layers: remove_spectral_norm(module.conv_1) remove_spectral_norm(module.conv_2) # toggle the state variable: self.spectral_norm_mode = False def forward(self, x): """ forward pass of the Generator :param x: input noise :return: *y => output of the generator at various scales """ from torch import tanh outputs = [] # initialize to empty list y = x # start the computational pipeline for block, converter in zip(self.layers, self.rgb_converters): y = block(y) outputs.append(tanh(converter(y))) return outputs class Discriminator(th.nn.Module): """ Discriminator of the GAN """ def turn_on_spectral_norm(self): """ private helper for turning on the spectral normalization :return: None (has side effect) """ from torch.nn.utils import spectral_norm if self.spectral_norm_mode is not None: assert self.spectral_norm_mode is False, \ "can't apply spectral_norm. It is already applied" # apply the same to the remaining relevant blocks for module in self.layers: module.conv_1 = spectral_norm(module.conv_1) module.conv_2 = spectral_norm(module.conv_2) # toggle the state variable: self.spectral_norm_mode = True def turn_off_spectral_norm(self): """ private helper for turning off the spectral normalization :return: None (has side effect) """ from torch.nn.utils import remove_spectral_norm if self.spectral_norm_mode is not None: assert self.spectral_norm_mode is True, \ "can't remove spectral_norm. It is not applied" # remove the applied spectral norm for module in self.layers: remove_spectral_norm(module.conv_1) remove_spectral_norm(module.conv_2) # toggle the state variable: self.spectral_norm_mode = False
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# Load modules from inferelator import inferelator_workflow, inferelator_verbose_level, MPControl, crossvalidation_workflow from inferelator.benchmarking.scenic import SCENICWorkflow, SCENICRegression from inferelator.distributed.inferelator_mp import MPControl # Set verbosity level to "Talky" inferelator_verbose_level(1) # Set the location of the input data and the desired location of the output files DATA_DIR = '~/repos/inferelator/data/yeast' OUTPUT_DIR = '/scratch/cj59/yeast_inference' PRIORS_FILE_NAME = 'YEASTRACT_20190713_BOTH.tsv' GOLD_STANDARD_FILE_NAME = 'gold_standard.tsv.gz' TF_LIST_FILE_NAME = 'tf_names.tsv' # Multiprocessing needs to be protected with the if __name__ == 'main' pragma if __name__ == '__main__': MPControl.set_multiprocess_engine("dask-cluster") MPControl.client.use_default_configuration("greene", n_jobs=2) MPControl.client.add_worker_conda("source /scratch/cgsb/gresham/no_backup/Chris/.conda/bin/activate scenic") MPControl.connect() # Define the general run parameters # Data Set 1 if __name__ == '__main__': # Create a worker worker = inferelator_workflow(regression=SCENICRegression, workflow=SCENICWorkflow) worker = set_up_workflow(worker) worker.set_expression_file(tsv="calico_expression_matrix_raw_microarray.tsv.gz") worker.set_file_properties(extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], metadata_handler="nonbranching") worker.adjacency_method = "grnboost2" worker.set_output_file_names(curve_data_file_name="metric_curve.tsv.gz") worker._do_preprocessing = False worker.do_scenic = False worker.append_to_path("output_dir", "set1_raw_grnboost") worker.run() # BBSR worker = inferelator_workflow(regression="bbsr", workflow="tfa") worker = set_up_workflow(worker) worker.set_expression_file(tsv="calico_expression_matrix_raw_microarray.tsv.gz") worker.set_file_properties(extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], metadata_handler="nonbranching") worker.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True, cv_split_ratio=0.2) worker.set_run_parameters(num_bootstraps=5) worker.append_to_path("output_dir", "set1_raw_bbsr") worker.set_output_file_names(curve_data_file_name="metric_curve.tsv.gz") cv_wrap = set_up_cv_seeds(worker) cv_wrap.run() del cv_wrap del worker # STARS-LASSO worker = inferelator_workflow(regression="stars", workflow="tfa") worker = set_up_workflow(worker) worker.set_expression_file(tsv="calico_expression_matrix_raw_microarray.tsv.gz") worker.set_file_properties(extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], metadata_handler="nonbranching") worker.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True, cv_split_ratio=0.2) worker.set_run_parameters(num_bootstraps=5) worker.append_to_path("output_dir", "set1_raw_stars") worker.set_output_file_names(curve_data_file_name="metric_curve.tsv.gz") cv_wrap = set_up_cv_seeds(worker) cv_wrap.run() del cv_wrap del worker # BBSR-BY-TASK worker = inferelator_workflow(regression="bbsr", workflow="multitask") worker = set_up_workflow(worker) # Calico data task task1 = worker.create_task(task_name="Calico_2019", expression_matrix_file="calico_expression_matrix_raw.tsv.gz", expression_matrix_columns_are_genes=True, extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], workflow_type="tfa", metadata_handler="nonbranching") # Kostya data task task2 = worker.create_task(task_name="Kostya_2019", expression_matrix_file="kostya_microarray_yeast.tsv.gz", expression_matrix_columns_are_genes=True, extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['isTs', 'is1stLast', 'prevCol', 'del.t', 'condName'], workflow_type="tfa", metadata_handler="branching") worker.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True, cv_split_ratio=0.2) worker.set_run_parameters(num_bootstraps=5) worker.append_to_path("output_dir", "set1_raw_joint_bbsr") cv_wrap = set_up_cv_seeds(worker) cv_wrap.run() del cv_wrap del worker # STARS-BY-TASK worker = inferelator_workflow(regression="stars", workflow="multitask") worker = set_up_workflow(worker) # Calico data task task1 = worker.create_task(task_name="Calico_2019", expression_matrix_file="calico_expression_matrix_raw.tsv.gz", expression_matrix_columns_are_genes=True, extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], workflow_type="tfa", metadata_handler="nonbranching") # Kostya data task task2 = worker.create_task(task_name="Kostya_2019", expression_matrix_file="kostya_microarray_yeast.tsv.gz", expression_matrix_columns_are_genes=True, extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['isTs', 'is1stLast', 'prevCol', 'del.t', 'condName'], workflow_type="tfa", metadata_handler="branching") worker.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True, cv_split_ratio=0.2) worker.set_run_parameters(num_bootstraps=5) worker.append_to_path("output_dir", "set1_raw_joint_stars") cv_wrap = set_up_cv_seeds(worker) cv_wrap.run() del cv_wrap del worker # AMUSR worker = inferelator_workflow(regression="amusr", workflow="multitask") worker = set_up_workflow(worker) # Calico data task task1 = worker.create_task(task_name="Calico_2019", expression_matrix_file="calico_expression_matrix_raw.tsv.gz", extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], workflow_type="tfa", metadata_handler="nonbranching") # Kostya data task task2 = worker.create_task(task_name="Kostya_2019", expression_matrix_file="kostya_microarray_yeast.tsv.gz", extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['isTs', 'is1stLast', 'prevCol', 'del.t', 'condName'], workflow_type="tfa", metadata_handler="branching") worker.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True, cv_split_ratio=0.2) worker.set_run_parameters(num_bootstraps=5, use_numba=True) worker.append_to_path("output_dir", "set1_raw_joint_amusr") cv_wrap = set_up_cv_seeds(worker) cv_wrap.run() del cv_wrap del worker """ # Create a worker worker = inferelator_workflow(regression=SCENICRegression, workflow=SCENICWorkflow) worker = set_up_workflow(worker) worker.set_expression_file(tsv="calico_expression_matrix_raw_microarray.tsv.gz") worker.set_file_properties(extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['TF', 'strain', 'date', 'restriction', 'mechanism', 'time'], metadata_handler="nonbranching") worker.adjacency_method = "genie3" worker.append_to_path("output_dir", "set1_genie3") worker.run() # Data Set 2 # Create a worker worker = inferelator_workflow(regression=SCENICRegression, workflow=SCENICWorkflow) worker = set_up_workflow(worker) worker.set_expression_file(tsv="kostya_microarray_yeast.tsv.gz") worker.set_file_properties(extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['isTs', 'is1stLast', 'prevCol', 'del.t', 'condName'], metadata_handler="branching") worker.adjacency_method = "grnboost2" worker.append_to_path("output_dir", "set2_grnboost") worker.run() # Create a worker worker = inferelator_workflow(regression=SCENICRegression, workflow=SCENICWorkflow) worker = set_up_workflow(worker) worker.set_expression_file(tsv="kostya_microarray_yeast.tsv.gz") worker.set_file_properties(extract_metadata_from_expression_matrix=True, expression_matrix_metadata=['isTs', 'is1stLast', 'prevCol', 'del.t', 'condName'], metadata_handler="branching") worker.adjacency_method = "genie3" worker.append_to_path("output_dir", "set2_genie3") worker.run() """
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18, 4943, 198, 220, 220, 220, 8383, 13, 5143, 3419, 198, 220, 220, 220, 37227, 198 ]
2.040959
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import os from flask_final.config import Debug, Secrets from flask_final import db, create_app is_env_var_set = os.getenv("SQLALCHEMY_DATABASE_URI") if not is_env_var_set: config = Secrets() else: config = Debug # Support for relative sqlite URIs if config.SQLALCHEMY_DATABASE_URI == "sqlite:///site.db": temp_app = create_app(config) config.SQLALCHEMY_DATABASE_URI = "sqlite:///" + os.path.join( temp_app.root_path, "site.db" ) app = create_app(config) from flask_script import Manager from flask_migrate import Migrate, MigrateCommand migrate = Migrate(app, db) manager = Manager(app) manager.add_command("db", MigrateCommand) if __name__ == "__main__": manager.run()
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2.59707
273
import numpy as np import numpy.ma as ma from numpy.testing import assert_array_equal import pytest import netCDF4 from cloudnetpy.categorize.lidar import Lidar WAVELENGTH = 900.0 @pytest.fixture(scope='session') def fake_lidar_file(tmpdir_factory): """Creates a simple lidar file for testing.""" file_name = tmpdir_factory.mktemp("data").join("radar_file.nc") root_grp = netCDF4.Dataset(file_name, "w", format="NETCDF4_CLASSIC") n_time, n_height = 4, 4 root_grp.createDimension('time', n_time) root_grp.createDimension('height', n_height) root_grp.createVariable('time', 'f8', 'time')[:] = np.arange(n_time) var = root_grp.createVariable('height', 'f8', 'height') var[:] = np.arange(n_height) var.units = 'km' root_grp.createVariable('wavelength', 'f8')[:] = WAVELENGTH root_grp.createVariable('latitude', 'f8')[:] = 60.43 root_grp.createVariable('longitude', 'f8')[:] = 25.4 var = root_grp.createVariable('altitude', 'f8') var[:] = 120.3 var.units = 'm' var = root_grp.createVariable('beta', 'f8', ('time', 'height')) var[:] = ma.array([[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]], dtype=float, mask=[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]) root_grp.close() return file_name
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