def run(self):
sample1 = pickle.load( gzip.open(self.sampleobjfile1, "rb") )
sample2 = pickle.load( gzip.open(self.sampleobjfile2, "rb") )
print self.size, os.path.basename(self.sampleobjfile1).split('.')[0], sample1.total, os.path.basename(self.sampleobjfile2).split('.')[0], sample2.total
#sampling "size" sequences from sample:
subsample1 = iseqlib.samplingSample( sample1, self.size ) #sampled sample
subsample2 = iseqlib.samplingSample( sample2, self.size ) #sampled sample
#Get different statistics:
stats = PairSamplingStats() #initialize stats for the current subsample
#Find Sizes of the Union of clones between subsample1 and subsample2:
counts1 = []
counts2 = []
for header, seq in subsample1.seqs.iteritems():
counts1.append( seq.count )
if header in subsample2.seqs:
counts2.append( subsample2.seqs[header].count )
else:
counts2.append( 0 )
for header, seq in subsample2.seqs.iteritems():
if header not in subsample1.seqs:
counts1.append( 0 )
counts2.append( seq.count )
if len(counts1) != len(counts2):
raise ValueError("The count vectors of two compared samples must have equal length. Found %d and %d\n" %(len(counts1), len(counts2)))
## Initialize the R interface
import rpy2.rinterface as rinterface
rinterface.set_initoptions(('rpy2', '--no-save'))
rinterface.initr()
import rpy2.robjects as robjs
from rpy2.robjects.packages import importr
vegan = importr('vegan')
vegdist = vegan.vegdist
counts = counts1
counts.extend(counts2)
rcountsVec = robjs.IntVector( counts ) #convert python list into R vector
rcountsMatrix = robjs.r['matrix'](rcountsVec, nrow = 2, byrow=True)
#indices = ['bray', 'horn', 'mountford', 'chao']
indices = self.options.similarityIndices
#"manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "morisita", "horn", "mountford", "raup" , "binomial" or "chao"
for index in indices:
disimilarity = vegdist( rcountsMatrix, method=index )
stats[index] = disimilarity[0]
#Write to temp file:
picklefile = os.path.join( self.outdir, "%d.pickle" % self.id)
pickle.dump( stats, gzip.open(picklefile, "wb") )
def run(self):
sample = pickle.load( gzip.open(self.sampleobjfile, "rb") )
#sampling "size" sequences from sample:
subsample = iseqlib.samplingSample( sample, self.size ) #sampled sample
#Get different statistics:
stats = SingleSamplingStats() #initialize stats for the current subsample
#1/ Number of uniq clones:
stats.uniqClones = len( subsample.seqs )
#2/ Diversity Indices
counts = [ seq.count for seq in subsample.seqs.values() ] #list of clone sizes
## Initialize the R interface
import rpy2.rinterface as rinterface
rinterface.set_initoptions(('rpy2', '--no-save'))
rinterface.initr()
import rpy2.robjects as robjs
from rpy2.robjects.packages import importr
vegan = importr('vegan')
rcounts = robjs.IntVector( counts ) #convert python list into R vector
##Diversity indices (Simpson, InverseSimpson, Shannon)
indices = self.options.diversityIndices
#['simpson', 'invsimpson', 'shannon']
for index in indices:
if index == 'uniqClones' or index == 'fisherAlpha':
continue
rval = vegan.diversity( rcounts, index )
stats[index] = rval[0]
## Fisher Alpha:
rfisher = vegan.fisher_alpha( rcounts )
stats.fisherAlpha = rfisher[0]
#Write to temp file:
picklefile = os.path.join( self.outdir, "%d.pickle" % self.id)
pickle.dump( stats, gzip.open(picklefile, "wb") )
def ready(self) -> None:
"""Perform initialization for back-end"""
logger.info(f"CATMAID version {settings.VERSION}")
# Make sure all settings variables are of the type we expect.
self.validate_configuration()
# If prepared statements are enabled, make sure they are created for
# every new connection. Binding this signal handler has to happen before
# the first database connection is created or connection pooling can not
# be used with prepared statements safely.
if settings.PREPARED_STATEMENTS:
db_signals.connection_created.connect(prepare_db_statements)
self.check_superuser()
# Make sure the existing version is what we expect
signals.pre_migrate.connect(check_old_version, sender=self)
# Validate CATMAID environment after all migrations have been run
signals.post_migrate.connect(validate_environment, sender=self)
# Register history checks
register(check_history_setup)
# Enable or disable spatial update notifications
register(check_spatial_update_setup)
# Make sure the expected default client instance settings are set.
register(check_client_settings)
# Test if output paths are accessible
register(check_media_path)
# Init R interface, which is used by some parts of CATMAID
if r_available:
rinterface.set_initoptions((b'rpy2', b'--no-save', b'--no-restore',
b'--no-init-file', b'--no-environ'))
rinterface.initr()
import rpy2.robjects as ro
from rpy2.robjects.packages import importr
import rpy2.rinterface as ri
ri.set_initoptions(('rpy2', '--verbose', '--no-save'))
ri.initr()
graphics = importr('graphics')
grdevices = importr('grDevices')
base = importr('base')
stats = importr('stats')
zoo = importr('zoo')
#Need to add params to importr as xts and quantmod have conflicts
xts = importr("xts", robject_translations = {".subset.xts": "_subset_xts2", "to.period": "to_period2"})
quantmod = importr('quantmod', robject_translations = {"skeleton.TA": "skeleton_TA2"})
AORD = ro.r('read.table("~/Documents/R/StrategyTester/Data/AORD.csv",header=T, sep=",")')
#WIP - using quantmod, zoo, xts in Python.
#Create Zoo object
#indexZoo = ro.r.rownames(AORD)
AORD = zoo.as_zoo(AORD)
AORD = xts.as_xts(AORD)
#Create MA zoo object
#Creating EMA using quantmod
chartData = AORD#.rx['2008-02::2008-08']
quantmod.chartSeries(chartData, theme="white")
EMA1=quantmod.addEMA(n=10,col=2)
import os
import string
import traceback
import rpy2.rinterface as rinterface
rinterface.set_initoptions(('rpy2', '--vanilla', '--max-ppsize=500000', '--quiet'))
import numpy
from subprocess import Popen, PIPE, STDOUT
import dendropy
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
import tempfile
from dendropy.interop import ape
import rpy2
from rpy2.robjects import numpy2ri
import math
import stopwatch
import multiprocessing as mp
from multiprocessing import Pool, current_process, Manager
from threading import Timer
import platform
import random
from itertools import izip
#mp_logger = mp.log_to_stderr()
#mp_logger.setLevel(mp.SUBDEBUG)
import logging
import pandas as pd
import time
#!/usr/bin/env python
from __future__ import division
import gc, sys, operator, scipy, datetime, multiprocessing, traceback
from scipy.special import comb
import talib as tl
import rpy2.rinterface as rinterface
rinterface.set_initoptions(('rpy2', '--max-ppsize=500000'))
rinterface.initr()
from rpy2 import robjects as ro
from rpy2.robjects import r
from rpy2.robjects.packages import importr
#import analysis.model_learning as ml
import data.stock_data_store as sd
import numpy as np
import utils.data_util as du
s = sd.StockDataStore()
global_ticker_data = dict()
counter = multiprocessing.Value("i", 0)
total = multiprocessing.Value("i", 0)
start_time = None
lock = multiprocessing.Lock()
def get_time_left(start_time, num_complete, total):
dtime = datetime.datetime.now() - start_time
time_per_ticker = dtime.total_seconds() / num_complete
diff = total - num_complete
return datetime.timedelta(seconds=int(time_per_ticker * diff))
#!/usr/bin/env python
from __future__ import division
import gc, sys, operator, scipy, datetime, multiprocessing, traceback
from scipy.special import comb
import talib as tl
import rpy2.rinterface as rinterface
rinterface.set_initoptions(('rpy2', '--max-ppsize=500000'))
rinterface.initr()
from rpy2 import robjects as ro
from rpy2.robjects import r
from rpy2.robjects.packages import importr
#import analysis.model_learning as ml
import data.stock_data_store as sd
import numpy as np
import utils.data_util as du
s = sd.StockDataStore()
global_ticker_data = dict()
counter = multiprocessing.Value("i", 0)
total = multiprocessing.Value("i", 0)
start_time = None
lock = multiprocessing.Lock()
def get_time_left(start_time, num_complete, total):
dtime = datetime.datetime.now() - start_time
time_per_ticker = dtime.total_seconds() /num_complete
diff = total - num_complete
return datetime.timedelta(seconds=int(time_per_ticker * diff))
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 02 11:38:19 2017
***** IT IS REALLY IMPORTANT TO NOTE THE RANGE OF CONFIGURABLES BELOW *****
@author: me
"""
import os
os.environ['R_HOME'] = 'C:/Progra~1/R/R-3.3.2/'
os.environ['R_USER'] = '******'
#os.environ['R_HOME']='C:\\Program Files\\R\\R-3.3.2\\bin\\x64\\'
import rpy2.rinterface as ri
try:
ri.set_initoptions(('rpy2', '--verbose', '--no-save'))
ri.initr()
except RuntimeError:
pass
lib_path = "'C:/Users/WINUSER/Documents/R/win-library/3.3'"
from rpy2.robjects import pandas2ri
pandas2ri.activate()
import pandas.rpy.common as common #This module will get deprecated at some point....
import rpy2.robjects as ro
import numpy as np
import pandas as pd
print ro.r(".libPaths(c(.libPaths()," + lib_path + "))")
def testSet_initoptions(self):
with self.assertRaises(RuntimeError):
rinterface.set_initoptions(('aa', '--verbose', '--no-save'))