misc.py

""" 
	This is a library for calculations Fisher matrices for GC.

	These is for miscellaneous functions that have nothing to do with cosmology.

	Markovic & Pourtsidou, 2016
"""

import time, datetime
from glob import glob
import numpy as np
import subprocess as sp

# A function to round to significant figures, not decimal places
def roundsf(x, n):
    mask = np.logical_or(np.equal(np.abs(x),np.inf), np.equal(x,0.0))
    decades = np.power(10.0,n-np.floor(np.log10(np.abs(x)))); decades[mask] = 1.0
    return np.round(np.array(x)*decades,0)/decades

# Generate a string timestamp
def get_timestamp():
	# Calculate the number of seconds since the Brexit referrendum polls closed
	t_Brexit = '23/06/2016 21:00' # GMT/UTC, 22:00 BST
	t_Brexit = time.mktime(datetime.datetime.strptime(t_Brexit, "%d/%m/%Y %H:%M").timetuple())
	return '-'+str(int(time.time() - t_Brexit))

# A function that reads in a Fisher matrix from a file
def readfish(filename):
	header = None
	with open(filename) as f:
		filestr = f.read().strip()
	if '#' in filestr:
		header = filestr.split('\n')[0]
		filestr = filestr.replace(header,'')
		parlist = header.replace('#','').strip().strip('"').split()
	else:
		raise Exception("No header in " + filename + "!")
	data = np.genfromtxt(filename)
	return np.matrix(data), parlist

# Function that returns a list of parameters, leaving only one list entry for every z-dependent parameter
# assumes the parameter name and redshift are separated by a '_' (an underscore)
def extract_pars(parlist, filename=False):
	Pchanged = False
	newpars = []
	for par in parlist:
		if 'lnPs' in par: 
			par = par.replace('lnPs', 'Ps')
			Pchanged = True
		par = par.split('_')[0]
		if par not in newpars: newpars.append(par)	
	if Pchanged:
		printstring = "I'm assuming you meant Ps, not lnPs"
		if filename: 
			printstring += " in "+filename+"!"
		else:
			printstring += "!"
		print printstring

	return newpars

# Function that returns a list of redshift bins in the Fisher matrix from a list of all the columns
# assumes the parameter name and redshift are separated by a '_' (an underscore)
def extract_zs(parlist):
	zs = []
	for par in parlist:
		pl = par.split('_')
		if len(pl)>1: 
			par = float(pl[1])
			if par not in zs: zs.append(par)	
	return zs

# A class that contains the Git environment at the time of it's initialisation.
# Currently it uses the subprocess module to speak to Git through the system.
#	Ideally some day it would use the GitPython module.
class GitEnv(object):

	# Optional input, /path/to/.git
	def __init__(self, git_dir=None):
		self.git_dir = git_dir
		self.hash, self.author, self.date = [str(s) for s in self.get_commit()]
		self.url = str(self.get_remote())
		self.branch = str(self.get_branch())
		self.repo = str(self.get_repo())
		self.printstart = ''
	# Also, should have an if that gives out the name of the parent folder + the
	# date and time in the case that it is NOT A GIT REPO!

	def __str__(self):
		startline = self.printstart
		as_string = startline + "This was generated by code from the Git repository at:"
		as_string += "\n" + startline + "\t " + self.url + ","
		as_string += "\n" + startline + "\t on the " + self.branch + " branch,"
		as_string += "\n" + startline + "\t with commit: " + self.hash
		as_string += "\n" + startline + "\t\t from " + self.date + ", "
		as_string += "\n" + startline + "\t\t by " + self.author + "."
		return as_string

	def set_print(self, startline):
		self.printstart = startline
	
	def get_git_cmd(self, args=[]):
		cmd = ['git']
		if self.git_dir != None:
			cmd.append('--git-dir')
			cmd.append(self.git_dir)
		for one in args:
			cmd.append(one)

		return cmd

	def get_hash(self, nochar=7, sep=''):
		return sep+self.hash[0:nochar]+sep
	
	# Get the hash, author and date of the most recent commit of the current repo.
	def get_commit(self):
		cmd = sp.Popen(self.get_git_cmd(['log', '-n','1']), stdout=sp.PIPE)
		cmd_out, cmd_err = cmd.communicate()
		newlist=[]
		for entry in cmd_out.strip().split('\n'):		
			if entry=='': continue
			entry = entry.split(' ')
			# This is a hack, should use a dict so can be sure what we are reading in:
			if 'commit' in entry[0] or 'Author' in entry[0] or 'Date' in entry[0]:
				newlist.append(' '.join(entry[1:]).strip())
		return newlist

	# At the moment this only gives the first url in what git returns.
	# Eventually it'd be nice if you could get the origin url, the fetch...
	def get_remote(self):
		cmd = sp.Popen(self.get_git_cmd(['remote', '-v']), stdout=sp.PIPE)
		cmd_out, cmd_err = cmd.communicate()
		if bool(cmd_out):
			try:
				return cmd_out.strip().split('https://')[1].split(' ')[0]
			except IndexError:
				ssh_url = cmd_out.strip().split('git@')[1].split(' ')[0]
				return ssh_url.replace(':','/')
		else:
			return 'no remote repo'

	def get_branch(self):
		cmd = sp.Popen(self.get_git_cmd(['branch']), stdout=sp.PIPE)
		cmd_out, cmd_err = cmd.communicate()
		branches = cmd_out.strip().splitlines()
		for branch in branches:
			if '*' in branch:
				return branch.replace('*','').strip()

	def get_repo(self):
		cmd = sp.Popen(self.get_git_cmd(['rev-parse','--show-toplevel']), stdout=sp.PIPE)
		cmd_out, cmd_err = cmd.communicate()
		return cmd_out.strip().split('/')[-1]