mcutils/mcutils.py

from __future__ import print_function,division
#import sys
#if (sys.version_info[0] < 3):
import numpy as np
from numpy import exp
import re
import codecs
import string
import scipy.signal
import functools
import types
import os
import pylab as plt
from itertools import chain
sqrt2=np.sqrt(2)


### COLORS, ETC ###
colors = None

nice_colors = (
# from http://www.mulinblog.com/a-color-palette-optimized-for-data-visualization/
    "#4D4D4D", # (gray)
    "#5DA5DA", # (blue)
    "#FAA43A", # (orange)
    "#60BD68", # (green)
    "#F17CB0", # (pink)
    "#B2912F", # (brown)
    "#B276B2", # (purple)
    "#DECF3F", # (yellow)
    "#F15854", # (red)
)

def colormap( list_of_colors ):
  from matplotlib.colors import colorConverter,LinearSegmentedColormap
  c = [ colorConverter.to_rgba(l) for l in list_of_colors ]
  # make the colormaps
  cmap = LinearSegmentedColormap.from_list('cmap',c,256)
  return cmap

def simpleaxis(ax=None):
    is ax is None: ax = plt.gca()
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    ax.get_xaxis().tick_bottom()
    ax.get_yaxis().tick_left()

def noaxis(ax=None):
    is ax is None: ax = plt.gca()
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    ax.spines['left'].set_visible(False)
    ax.spines['bottom'].set_visible(False)

def xrayAttLenght(*args,**kw):
  from periodictable import xsf
  n = xsf.index_of_refraction(*args,**kw)
  if not "wavelength" in kw:
    wavelength = 12.398/np.asarray(kw["energy"])
  else:
    wavelength = np.asarray(kw["wavelength"])
  attenuation_length = np.abs( (wavelength*1e-10)/ (4*np.pi*np.imag(n)) )
  return attenuation_length


def xrayFluo(atom,density,energy=7.,length=30.,I0=1e10,\
        det_radius=1.,det_dist=10.,det_material="Si",det_thick=300,verbose=True):
  """ compound: anything periodictable would understand 
      density:  in mM
      length: sample length in um
      energy: in keV, could be array
  """
  import periodictable
  from periodictable import xsf
  wavelength = 12.398/energy
  atom = periodictable.__dict__[atom]
  # 1e3 -> from mM to M
  # 1e3 -> from L to cm3
  # so 1 mM = 1e-3M/L = 1e-6 M/cm3
  density_g_cm3 = density*1e-6*atom.mass
  n = xsf.index_of_refraction(atom,density=density_g_cm3,wavelength=wavelength)
  attenuation_length = xrayAttLenght( atom,density=density_g_cm3,energy=energy )
  # um-> m: 1e-6
  fraction_absorbed = 1.-np.exp(-length*1e-6/attenuation_length)
  if verbose:
    print("Fraction of x-ray photons absorbed by the sample:",fraction_absorbed)
  ## detector ##
  det_area = np.pi*det_radius**2
  det_solid_angle = det_area/(4*np.pi*det_dist**2)
  if verbose:
    print("Detector fraction of solid angle:",det_solid_angle)
  det_att_len = xrayAttLenght(det_material,wavelength=atom.K_alpha)
  det_abs     = 1-np.exp(-det_thick*1e-6/det_att_len)
  if verbose:
    print("Detector efficiency (assuming E fluo = E_K_alpha):",det_abs)
  eff = fraction_absorbed*det_solid_angle*det_abs
  if verbose:
    print("Overall intensity (as ratio to incoming one):",eff)
  return eff


def pulseDuration(t0,L,GVD):
  return t0*np.sqrt( 1.+(L/(t0**2/2/np.abs(GVD))))

class MCError(Exception):
  def __init__(self, value):
    self.value = value
  def __str__(self):
    return repr(self.value)


### VECTOR ... ETC. ###

def vectorLenght(v):
  """ assuming axis -1 as coord """
  return np.sqrt(np.sum(v*v,axis=-1))

def versor(v):
  return v/vectorLenght(v)[:,np.newaxis]


### LIST,INDEXING ... ETC. ###

def smartIdx(idx,forceContigous=False):
  """ Try to interpret an array of bool as slice;
  this allows selecting a subarray alot more efficient 
  since array[slice] it returns a view and not a copy """
  if (isinstance(idx,int)):
    ret = slice(idx,idx+1)
  elif (isinstance(idx,slice)):
    ret = idx
  else:
    idx = np.asarray(idx)
    if idx.dtype == np.bool:
      i = np.where(idx)[0]
    else:
      i = idx
    # in case there is only one
    if (len(i) == 1):
      ret = slice(i[0],i[0]+1)
      return ret
    if forceContigous:
      ret = slice(i[0],i[-1])
    else:
      d = i[1:]-i[0:-1]
      dmean = int(d.mean())
      if np.all(d==dmean):
        ret = slice(i[0],i[-1]+1,dmean)
      else:
        ret = idx
  return ret


### CONVOLUTION,INTERPOLATION,SMOOTHING ... ETC. ###

def poly_approximant(x,y,order=10,allowExtrapolation=False,fill_value=0):
  """ return a polinomial view """
  poly = np.polyfit(x,y,order)
  def f(xx):
    res = np.polyval(poly,xx)
    if allowExtrapolation:
      return res
    else:
      if np.isscalar(xx) and ( ( xx>x.max()) or (xx<x.min() ) ):
        return fill_value
      elif not np.isscalar(xx):
        idx = (xx<x.min()) | (xx>x.max() )
        res[idx] = fill_value
      return res
  return f


def smoothing(x,y,err=None,k=5,s=None,newx=None,derivative_order=0):
  idx = np.isnan(x)|np.isnan(y)
  idx = ~ idx
  if newx is None: newx=x
  if idx.sum() > 0:
    x=x[idx]
    y=y[idx]
  if idx.sum() < 3:
    return np.ones(len(newx))
  if err is None:
    w=None
  elif err == "auto":
    n=len(x)
    imin = max(0,n/2-20)
    imax = min(n,n/2+20)
    idx = range(imin,imax)
    p = np.polyfit(x[idx],y[idx],4)
    e = np.std( y[idx] - np.polyval(p,x[idx] ) )
    w = np.ones_like(x)/e
  else:
    w=np.ones_like(x)/err
  from scipy.interpolate import UnivariateSpline
  if (s is not None):
    s = len(x)*s
  s = UnivariateSpline(x, y,w=w, k=k,s=s)
  if (derivative_order==0):
    return s(newx)
  else:
    try:
      len(derivative_order)
      return [s.derivative(d)(newx) for d in derivative_order]
    except:
      return s.derivative(derivative_order)(newx)


def interpolator(x,y,kind='linear',axis=-1, copy=False, bounds_error=False, fill_value=np.nan):
  from scipy import interpolate
  if (kind != "linear"):
    print("Warning interp1d can be VERY SLOW when using something that is not liear")
  f = interpolate.interp1d(x,y,kind=kind,axis=axis,copy=copy,bounds_error=bounds_error,fill_value=fill_value)
  return f

def interpolator_spl(x,y,kind="cubic"):
  from scipy import interpolate as itp
  if kind == "linear": kind=1
  if kind == "cubic" : kind=3
  splinepars = itp.splrep(x,y,k=kind)
  def f(x,der=0,):
    """f(x) returns values for x[i]. f(x,order) return order-th derivative"""
    return itp.splev(x,splinepars,der=der)
  return f

def interpolate_fast(x,y,newx,kind='cubic'):
  f = interpolator_spl(x,y,kind=kind)
  return f(newx)

def interpolate(x,y,newx,kind='linear',axis=-1, copy=False, bounds_error=False, fill_value=np.nan):
  f = interpolator(x,y,kind=kind,axis=axis,copy=copy,bounds_error=bounds_error,fill_value=fill_value)
  return f(newx)

def getElement(a,i,axis=-1):
  nDim = a.ndim
  if (axis<0): axis = nDim+axis
  colon = (slice(None),)
  return a[colon*axis+(i,)+colon*(nDim-axis-1)]

def setElement(a,i,res,axis=-1):
  temp = getElement(a,i,axis=axis)
  np.copyto(temp,res)

def invertedView(x):
  return x[ slice(None,None,-1) ]

def convolveQuad(x,y,xres,yres,useAutoCrop=True,
        fill_value=0.,axis=-1):
  print("NOT FINISHED")
  return
  from scipy import integrate
  if (useAutoCrop):
    idxRes = smartIdx( yres>(1e-4*yres.max()) )
    #print("Autocropping",idxRes,xres.shape)
  else:
    idxRes = slice(None)
  xresInv =  -invertedView( xres[idxRes] ) 
  yresInv =   invertedView( yres[idxRes] )
  area    =  integrate.simps(yres,x=xres)

  f = interpolator(x,y)
  r = interpolator(xres,yres)

  if y.ndim < 2: y = y[np.newaxis,:]
  nDim = y.ndim
  if (axis<0): axis = nDim+axis

  ## expand yres to allow broadcasting
  sh = [1,]*y.ndim
  sh[axis] = len(yres)
  yres = yres.reshape(sh)
  
  ## prepare output
  out = np.empty_like(y)
  nP = len(x)
  for i in range(nP):
    # interpolate x,y on xres+x[i]
    x_integral = xresInv+x[i]
    ytemp = interpolate(x,y,x_integral,fill_value=fill_value,axis=axis)/area
    # do integration
    res = integrate.simps(ytemp*yresInv,x=xresInv+x[i],axis=axis)
    colon = (slice(None),)
    setElement(out,i,res,axis=axis)
  return out


def convolve(x,y,xres,yres,useAutoCrop=True,approximantOrder=None,fill_value=0.,axis=-1):
  """ if approximantOrder is not None, use interpolating polynomial of order
      approximantOrder to perform integration """
  from scipy import integrate
  import copy
  if (useAutoCrop):
    idxRes = smartIdx( yres>(1e-4*yres.max()) )
    #print("Autocropping",idxRes,xres.shape)
  else:
    idxRes = slice(None)
  xresInv =  -invertedView( xres[idxRes] ) 
  yresInv =   invertedView( yres[idxRes] )
  area    =  integrate.simps(yres,x=xres)

  if approximantOrder is not None:
    #print("Using approximant!!",xresInv.shape)
    approx = poly_approximant(xresInv,yresInv/area,approximantOrder,
            allowExtrapolation=False,fill_value=0)
    #return approx,xresInv,yresInv
    return convolveFunc(x,y,approx,fill_value=fill_value,axis=axis,)

  if y.ndim < 2: y = y[np.newaxis,:]
  nDim = y.ndim
  if (axis<0): axis = nDim+axis

  ## expand yres to allow broadcasting
  sh = [1,]*y.ndim
  sh[axis] = len(yres)
  yres = yres.reshape(sh)
  
  ## prepare output
  out = np.empty_like(y)
  nP = len(x)
  f = interpolator(x,y,fill_value=fill_value,axis=axis)
  for i in range(nP):
    # interpolate x,y on xres+x[i]
    x_integral = xresInv+x[i]
    ytemp = f(x_integral)/area
    #ytemp  = interpolate(x,y,x_integral,fill_value=fill_value,axis=axis)/area
    #ytemp = f(x_integral)/area
    # do integration
    res = integrate.simps( np.transpose(ytemp.T*yresInv),x=xresInv+x[i],axis=axis)
    colon = (slice(None),)
    setElement(out,i,res,axis=axis)
  return out


def fftconvolve(x,y,yres,xres=None,normalize=False):
  if (xres is not None):
    yres = interpolate(xres,yres,x,fill_value=0)
  fft  = scipy.signal.fftconvolve(y,yres,"full")
  _idx = np.argmin( np.abs(x) ); # find t=0
  fft  = fft[_idx:_idx+len(x)]
  if normalize:
    norm = fftconvolve_find_norm(x,yres,xres=None)
  else:
    norm = 1
  return fft/norm

def fftconvolve_find_norm(x,res,xres=None):
  step = np.ones_like(x)
  n = int( len(step)/2 )
  step[:n] = 0
  norm = fftconvolve(x,step,res,xres=xres,normalize=False).max()
  return norm

def convolveGaussian(x,y,sig=1.,nPointGaussian=51,fill_value=0.,axis=-1):
  xG = np.linspace(-5*sig,5*sig,nPointGaussian)
  G  = gaussian(xG,x0=0,sig=sig)
  return convolve(x,y,xG,G,fill_value=fill_value,axis=axis)


def convolveFunc(x,y,func_res,fill_value=0.,axis=-1):
  from scipy import integrate
  if y.ndim < 2: y = y[np.newaxis,:]
  nDim = y.ndim
  if (axis<0): axis = nDim+axis

  ## prepare output
  out = np.empty_like(y)

  nP = len(x)
  for i in range(nP):
    # calculate the values of the resolution function on x-x[i]
    ytemp = func_res(x-x[i])
    # do integration
    res = integrate.simps(y*ytemp,x=x-x[i],axis=axis)
    setElement(out,i,res,axis=axis)
  return out

def convolveFuncParams(x,y,func_res,func_res_pars,fill_value=0.,axis=-1):
  def tempFunc(xx):
    return func_res(xx,*func_res_pars)
  return convolveFunc(x,y,tempFunc,fill_value=fill_value,axis=axis)

def convolve_test(nG=51):
  import time
  x=np.arange(100)
  y=(x>50).astype(np.float)
  sig = 3
  xG = np.linspace(-5*sig,5*sig,nG)
  G  = gaussian(xG,x0=0,sig=sig)
  Gpoly = np.polyfit(xG,G,20)
  t0 = time.time()
  conv_num = convolve(x,y,xG,G,fill_value=0.)
  print("Num:",time.time()-t0)
  t0 = time.time()
  conv_poly = convolve(x,y,xG,G,approximantOrder=10,fill_value=0.)
  print("Num:",time.time()-t0)
  t0 = time.time()
  conv_fun = convolveFuncParams(x,y,gaussian,(0,sig),fill_value=0.)
  print("Fun:",time.time()-t0)
  import pylab as plt
  plt.plot(conv_num.T,label="Numerical %d points" % nG)
  plt.plot(conv_fun.T,"o",label="Gaussian F")
  plt.plot(conv_poly.T,label="Gaussian (poly)")
  plt.plot(conv_num.T-conv_fun.T)
  return conv_num,conv_fun


def conv_gauss_and_const(x,sig):
  from scipy.special import erf
  return 0.5*(1-erf(-x/sqrt2/sig))

def conv_gauss_and_exp(x,sig,tau):
  from scipy.special import erf
  #from mpmath import erf
  #http://www.numberempire.com/integralcalculator.php?function=exp%28-x%2Fl%29*exp%28-%28t-x%29**2%2F2%2Fs**2%29%2FSqrt%282%29%2FSqrt%28pi%29%2Fs&var=x&answers=
  # actually calculated with sympy 
  #return -(erf(sqrt2*(sig**2 - x*tau)/(2*sig*tau)) - 1)*exp(sig**2/(2*tau**2) - x/tau)/2
  return 0.5*np.exp(-(2*tau*x-sig**2)/2/tau**2)*(1-erf( (-tau*x+sig**2)/sqrt2/tau/sig))

def gaussian(x,x0=0,sig=1,normalize=True):
  g =   np.exp(-(x-x0)**2/2/sig**2)
  if normalize:
    return 1/np.sqrt(2*np.pi)/sig*g
  else:
    return g


## FFT filter ##
class FFTfilter(object):
  def __init__(self,s,dx=1,wins=((0.024,0.01),),wintype="gauss"):
    f,ffts = fft(s,dx=dx)
    filter = np.ones_like(f)
    for win in wins:
      if wintype == "gauss":
        filter *= (1-gaussian(f,win[0],win[1],normalize=False))
        filter *= (1-gaussian(f,-win[0],win[1],normalize=False))
      else:
        print("Not implemented")
    
    self.filter=filter

  def apply(self,s):
    s = np.fft.fft(s)
    return np.fft.ifft(s*self.filter)
    

### PROMPT,PROCESS,TIME,DATE ... ETC. ###

class procCom(object):
  def __init__(self,cmd):
    import pexpect
    self.proc = pexpect.spawn(cmd)

  def get(self,timeout=None,waitFor=None):
    import pexpect
    if (waitFor is not None):
      s = ""
      try:
        while s.find(waitFor)<0:
          s+=self.proc.read_nonblocking(timeout=timeout)
      except (pexpect.TIMEOUT,pexpect.EOF):
        pass
    else: 
      s=""
      try:
        while 1:
          s+=self.proc.read_nonblocking(timeout=timeout)
      except (pexpect.TIMEOUT,pexpect.EOF):
        pass
    #print "got",s
    return s

  def send(self,what):
    self.proc.write(what)
    self.proc.flush()
    #print "send",what

  def query(self,what,timeout=None,waitFor=None):
    self.send(what)
    return self,get(timeout=timeout,waitFor=waitFor)

def getCMD(cmd,strip=True):
  import os
  shell = os.popen(cmd)
  ret = shell.readlines()
  shell.close()
  if (strip):
    ret = [x.strip() for x in ret]
  return ret

def lsdir(path,withQuotes=False,recursive=False):
  if recursive:
    dirs = []
    for (dir, _, file) in os.walk(path): dirs.append(dir)
  else:
    content = getCMD("ls -1 %s" % path)
    content = ["%s/%s" % (path,x) for x in content]
    dirs    = [x for x in content if os.path.isdir(x)]
  if (withQuotes):
    dirs = [ "'%s'" % x for x in dirs ]
  return dirs


def lsfiles(path,withQuotes=False,recursive=False):
  if recursive:
    print("Not sure is working")
    files = []
    for (dir, _, file) in os.walk(path): files.append(file)
  else:
    content = getCMD("ls -1 %s" % path)
    content = ["%s/%s" % (path,x) for x in content]
    files   = [x for x in content if os.path.isfile(x)]
  if (withQuotes):
    files = [ "'%s'" % x for x in files ]
  return files

def downloadPDB(pdbID,outFileName=None):
  import urllib2
  import os
  address =  "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=%s" % pdbID
  p = urllib2.urlopen(address)
  lines = p.readlines()
  if (outFileName is None):
    outFileName = pdbID+".pdb"
  folder = os.path.dirname(outFileName)
  if (folder != '' and not os.path.exists(folder)):
    os.makedirs(folder)
  f=open(outFileName,"w")
  f.write( "".join(lines) )
  f.close()


def dateStringToObj(s,format="%Y.%m.%d %H:%M:%S"):
  import datetime
  return datetime.datetime.strptime(s,format)

def now():
  import time
  return time.strftime("%Y.%m.%d %H:%M:%S",time.localtime())

def mytimer(func,args):
  import time
  t0=time.time()
  ret=func(*args)
  return time.time()-t0,ret

### TXT I/O ###

def lineToVals(line):
  return map(eval,string.split(line))

class DataFile(object):
  filename=""
  lines=[]
  comments=[]
  head={}
  Data=[]
  Ndata=0

  def __init__(self,f):
    self.filename=f
    self.Read()

  def Read(self):
    f=open(self.filename,"r")
    temp = f.readlines();
    f.close();
    r=re.compile('\s+');
    c=re.compile('^\s*#');
    for l in temp:
      if (re.match(c,l)):
        self.comments.append(l)
      else:
        self.lines.append(l)
    # first of non commented line might be header
    # try to understand it
    keys = []
    try:
      v=lineToVals(self.lines[0])
      for i in range(len(v)):
        keys.append(i)
    except:
        keys=self.lines[0].split()
        self.lines.remove( self.lines[0] )
    datatemp = []
    for l in self.lines:
      datatemp.append( lineToVals(l) )
    self.Data = np.asarray(datatemp)
    for i in range(len(keys)):
      self.head[keys[i]] = self.Data[:,i]
      self.__dict__[keys[i]] = self.Data[:,i]
    (self.Ndata,self.Ncol) = self.Data.shape
    
  def clean(self):
    del self.Data


def writev(fname,x,Ys,form="%+.6g",sep=" ",header=None,headerv=None):
  """ Write data to file 'fname' in text format.
      Inputs:
        x = x vector
        Ys = vector(or array or list of vectors) for the Ys
        form = format to use
        sep = separator
        header = text header (must be a string)
        headerv = vector to be used as header, it is convienient when
          the output must be of the form
            Ncol 252 253 254
            x1   y11 y12 y13
            .......
          In this case headerv should be [252,253,254]
  """
  if (type(x) != np.ndarray): x=np.array(x)
  if (type(Ys) != np.ndarray): Ys=np.array(Ys)
  if (len(Ys.shape)==1):
    Ys=Ys.reshape(Ys.shape[0],1)
  nx = len(x)
  if (Ys.shape[0] == nx):
    ny=Ys.shape[1]
  elif (Ys.shape[1] == nx):
    ny=Ys.shape[0]
    Ys=np.transpose(Ys)
  else:
    raise MCError("dimension of x (%d) does not match any of the dimensions of Ys (%d,%d)" % (nx,Ys.shape[0],Ys.shape[1]))
  f=codecs.open(fname,encoding='utf-8',mode="w")
  if (header is not None):
    f.write(header.strip()+"\n")
  if (headerv is not None):
    f.write("%d" % (ny+1))
    for i in range(ny):
      f.write(sep)
      f.write(form % headerv[i])
    f.write("\n")
  for i in range(nx):
    f.write(form % x[i])
    f.write(sep)
    for j in range(ny-1):
      f.write(form % Ys[i,j])
      f.write(sep)
    f.write(form % Ys[i,-1])
    f.write("\n")
  f.close()


def writev(fname,x,Ys,form="%+.6g",sep=" ",header=None,headerv=None):
  """ Write data to file 'fname' in text format.
      Inputs:
        x = x vector
        Ys = vector(or array or list of vectors) for the Ys
        form = format to use
        sep = separator
        header = text header (must be a string)
        headerv = vector to be used as header, it is convienient when
          the output must be of the form
            Ncol 252 253 254
            x1   y11 y12 y13
            .......
          In this case headerv should be [252,253,254]
  """
  if (type(x) != np.ndarray): x=np.array(x)
  if (type(Ys) != np.ndarray): Ys=np.array(Ys)
  if (len(Ys.shape)==1):
    Ys=Ys.reshape(Ys.shape[0],1)
  nx = len(x)
  if (Ys.shape[1] == nx):
    ny=Ys.shape[0]
  elif (Ys.shape[0] == nx):
    ny=Ys.shape[1]
    Ys=np.transpose(Ys)
  else:
    raise MCError("dimension of x (%d) does not match any of the dimensions of Ys (%d,%d)" % (nx,Ys.shape[0],Ys.shape[1]))
  f=codecs.open(fname,encoding='utf-8',mode="w")
  if (header is not None):
    f.write(header.strip()+"\n")
  if (headerv is not None):
    f.write("%d" % (ny+1))
    for i in range(ny):
      f.write(sep)
      f.write(form % headerv[i])
    f.write("\n")
  out = np.vstack( (x,Ys) )
  np.savetxt(f,np.transpose(out),fmt=form,delimiter=sep)

def loadtxt(fname,hasVectorHeader=True,asObj=False,isRecArray=False):
  if (isRecArray):
    return loadRecArray(fname,asObj=asObj)
  a=np.loadtxt(fname)
  if (not hasVectorHeader):
    x = a[:,0]
    y = a[:,1:].T
    t = None
  else:
    x = a[1:,0]
    y = a[1:,1:].T
    t = a[0,1:]
  if (asObj):
    class txtFile(object):
      def __init__(self,x,y,t):
        self.x = x
        self.y = y
        self.t = t
    return txtFile(x,y,t)
  else:
    return x,y,t

def loadRecArray(fname,hasVectorHeader=True,asObj=False):
  a=np.loadtxt(fname,skiprows=1)
  # find header
  f=open(fname,"r")
  found = None
  while found is None:
    s=f.readline().strip()
    if s[0] != "#":
      found = s
  names = found.split()
  if (asObj):
    class txtFile(object):
      def __init__(self):
        pass
    ret = txtFile()
    for i in range(len(names)):
      ret.__dict__[names[i]] = a[:,i]
  else:
    ret = np.core.records.fromarrays(a.transpose(),names=",".join(names))
  return ret


def prepareRecArrayFromDict( mydict,n=1,leaveEmpty=True ):
   names   = mydict.keys()
   formats = [ type(mydict[p]) for p in names ]
   if leaveEmpty:
     array_kind = np.empty
   else:
     array_kind = np.zeros
   return array_kind(n, dtype={'names':names, 'formats':formats})

def prepareRecArrayFromNamesAndArray( names,ar,n=1,leaveEmpty=True ):
   formats = [ ar.dtype.type for p in names ]
   if leaveEmpty:
     array_kind = np.empty
   else:
     array_kind = np.zeros
   return array_kind(n, dtype={'names':names, 'formats':formats})



def writeMatrix(fout,M,x,y,form="%+.6g",sep=" ",header=None):
  (nx,ny) = M.shape
  if ( (nx == len(x)) and (ny==len(y)) ):
    pass
  elif ( (nx == len(y)) and (ny==len(x)) ):
    M=M.transpose()
    (nx,ny) = M.shape
  else:
    e  = "Dimensions of matrix and the x or y vectors don't match"
    e += "shapes of M, x, y: " + str(M.shape) + " " +str(len(x))+ " " +str(len(y))
    raise MCError(e)
  temp = np.zeros( (nx+1,ny) )
  temp[1:,:] = M
  temp[0,:] = y
  writev(fout,np.hstack( (0,x) ),temp,form=form,sep=sep,header=header)


### MATPLOTLIB ... ETC. ###

def lt(i,style="-"):
  colors="rkbgy"
  i = i%len(colors)
  color = colors[i]
  if (style is not None): color += style
  return color

def displayFig(i,x=None,y=None,roi=None):
  import pylab as plt
  from matplotlib.widgets import Slider, Button, RadioButtons
  fig=plt.figure()
  n1,n2=i.shape
  if x is None:
    x = np.arange(n1)
  if y is None:
    y = np.arange(n2)

  ax = fig.add_subplot(111)
  if roi is not None:
    (x1,x2,y1,y2) = roi
  else:
    x1,x2,y1,y2 = (0,n1,0,n2)
  xm=x[x1]; xM=x[x2-1]
  ym=y[y1]; yM=y[y2-1]
  def _format_coord(x, y):
    col = int(x+0.5)
    row = int(y+0.5)
    if col>=0 and col<n2 and row>=0 and row<n1:
      z = i[row,col]
      return 'x=%1.4f, y=%1.4f, z=%1.4f'%(x, y, z)
    else:
      return 'x=%1.4f, y=%1.4f'%(x, y)
  iplot = i[x1:x2,y1:y2]
  im1=ax.imshow(iplot,origin='bottom',extent=[xm,xM,ym,yM])
  ax.format_coord = _format_coord
  fig.subplots_adjust(left=0.25, bottom=0.25)
  fig.colorbar(im1)
  axcolor = 'lightgoldenrodyellow'
  axmin = fig.add_axes([0.25, 0.1, 0.65, 0.03], axisbg=axcolor)
  axmax  = fig.add_axes([0.25, 0.15, 0.65, 0.03], axisbg=axcolor)
  smin = Slider(axmin, 'Min', -5000, 5000, valinit=-200)
  smax = Slider(axmax, 'Max', -5000, 5000, valinit=200)

  def update(val):
    im1.set_clim([smin.val,smax.val])
    fig.canvas.draw()
  smin.on_changed(update)
  smax.on_changed(update)


def savefig(fname,figsize,fig=None,**kwargs):
  """ 
    force saving figure with a given size, useful when using tiling wm;
    if fname is a list, it saves multiple files, for example [todel.pdf,todel.png]
  """
  if isinstance(fname,str): fname = (fname,)
  if fig is None: fig = plt.gcf()
  old_bkg = plt.get_backend()
  old_inter = plt.isinteractive()
  try:
    plt.switch_backend("cairo")
    old_height = fig.get_figheight()
    old_width  = fig.get_figwidth()
    fig.set_figwidth ( figsize[0] )
    fig.set_figheight( figsize[1] )
    [  fig.savefig(f,**kwargs) for f in fname ]
    plt.switch_backend(old_bkg)
  finally:
    plt.switch_backend(old_bkg)
    plt.interactive(old_inter)

### FFT ###

def fft(y,dx=1):
  fft = np.fft.fft(y)
  f   = np.fft.fftfreq(len(y),d=dx)
  return f,fft
  
def wrap(vec,at_idx):
  """ wrap vector at such that at_idx corresponds to the center
      it might be useful for FFT (should try to implemente it using np.roll)"""
  nhalf = int(len(vec)/2)
  if (at_idx>nhalf):
    vec = np.concatenate( (vec[at_idx-nhalf:],vec[:at_idx-nhalf] ))
  else:
    vec = np.concatenate( (vec[at_idx+nhalf:],vec[:at_idx+nhalf]))
  return vec

### REBIN, RUNNING AVG, ... ETC ###

def rebinOLD(bins_edges,x,*Y):
  """ rebins a list of Y based on x using bin_edges
      returns 
        center of bins (vector)
        rebinned Y     (list of vectors)
        Simga's        (list of vectors), note: just std not std of average
        N              (list of vectors), number of occurrances
  """
  n=len(bins_edges)-1
  outX = []
  outY = []
  outS = []
  outN = []
  for j in range(len(Y)):
    outY.append(np.empty(n))
    outS.append(np.empty(n))
    outN.append(np.empty(n))
  outX = np.empty(n)
  for i in range(n):
    idx = (x>=bins_edges[i]) & (x<bins_edges[i+1])
    outX[i] = (bins_edges[i]+bins_edges[i+1])/2.
    print("IDX",i,idx.sum(),outX[i])
    if (idx.sum() > 0):
      for j in range(len(Y)):
        outN[j][i] = idx.sum()
        outY[j][i] = Y[j][idx].mean()
        outS[j][i] = Y[j][idx].std()
    else:
      for j in range(len(Y)):
        outN[j][i] = 0
        outY[j][i] = np.nan
        outS[j][i] = np.nan
  return outX,outY,outS,outN

def rebin1D(a,shape):
   sh = shape,a.shape[0]//shape
   return a.reshape(sh).mean(1)

def rebin1Dnew(a,shape):
  n0 = a.shape[0]//shape
  sh = shape,n0
  return a[:n0*shape].reshape(sh).mean(1)

def rebin2D(a, shape):
    sh = shape[0],a.shape[0]//shape[0],shape[1],a.shape[1]//shape[1]
    return a.reshape(sh).mean(-1).mean(1)

def rebin2Dnew(a, shape):
  # // means floor 
  n0 = a.shape[0]//shape[0]
  n1 = a.shape[1]//shape[1]
  crop = shape[0]*n0,shape[1]*n1
  sh = shape[0],n0,shape[1],n1
  #print a[:n0*shape[0],:n1*shape[1]].reshape(sh)
  return a[:crop[0],:crop[1]].reshape(sh).mean(-1).mean(1)

def rebin3Dnew(a, shape):
  # // means floor 
  n0 = a.shape[0]//shape[0]
  n1 = a.shape[1]//shape[1]
  n2 = a.shape[2]//shape[2]
  sh = shape[0],n0,shape[1],n1,shape[2],n2
  crop = n0*shape[0],n1*shape[1],n2*shape[2]
  #print a[:n0*shape[0],:n1*shape[1]].reshape(sh)
  return a[:crop[0],:crop[1],:crop[2]].reshape(sh).mean(-1).mean(-2).mean(-3)

def rebin(a, shape):
  a = np.asarray(a)
  ndim = a.ndim
  if (ndim == 1):
    return rebin1Dnew(a,shape)
  elif (ndim == 2):
    return rebin2Dnew(a,shape)
  elif (ndim == 3):
    return rebin3Dnew(a,shape)
  else:
    print("Can't do rebin of",a)


def rebinTODO(a, shape):
  ndim = a.ndim
  if (len(shape) != ndim):
    print("Error, asked to rebin a %d dimensional array but provided shape with %d lengths" % (ndim,len(shape)))
    return None
  nout = []
  for n in range(ndim):
    nout.append( a.shape[n]%shape[n] )
  print("Not implemented ...")

### DISTRIBUTION, MEDIAN, SIGMA, ETC. ###

def idx_within_std_from_center(vector,range):
  (m,s) = MedianAndSigma(vector)
  return np.abs(vector-m)<(range*s)

def MedianAndSigma(a):
  median = np.median(a)
  MAD    = np.median(np.abs(a-median))
  sigma  = 1.4826*MAD; # this assumes gauss distribution
  return (median,sigma)

def weigthed_average(y,e=None,axis=0):
  if e is None:
    e=np.ones_like(y)
  if (axis != 0):
    y = y.transpose()
    e = e.transpose()
  (n0,n1) = y.shape
  yout = np.empty(n1)
  eout = np.empty(n1)
  for i in range(n1):
    toav = y[:,i]
    valid = np.isfinite(toav)
    toav = toav[valid]
    w    = 1/e[valid,i]**2
    yout[i] = np.sum(toav*w)/np.sum(w)
    eout[i] = np.sqrt(1/np.sum(w))
  return yout,eout

### CONVERSION ###
def convert(value=1,unit="eV",out="nm"):
  if (unit == "eV") & (out =="nm"):
    return 1239.8/value


### IMINUIT RELATED ###

def iminuitClass(modelFunc):
  """ build a class to help fitting, first argumes of modelFunc should be x"""
  import inspect
  import iminuit
  import iminuit.util
  args = inspect.getargspec(modelFunc).args
  defaults = inspect.getargspec(modelFunc).defaults
  if defaults is not None:
    nDef = len( defaults )
    args = args[:-nDef]
  args_str = ",".join(args[1:])
  

  class iminuitFit(object):
    def __init__(self,x,data,init_pars,err=1.):
      self.x = x
      self.data = data
      self.err  = err
      self.init_pars=init_pars
      self.func_code = iminuit.util.make_func_code(args[1:])#docking off independent variable
      self.func_defaults = None #this keeps np.vectorize happy

    def __call__(self,*arg):
      return self.chi2(*arg)

    def model(self,*arg):
      return modelFunc(self.x,*arg)

    def chi2(self,*arg):
      c2 = (self.model(*arg)-self.data)/self.err
      return np.sum(c2*c2)

    def fit(self,showInit=True,showPlot=True,doFit=True,doMinos=False):
      import pylab as plt
      p = self.init_pars
      if "errordef" not in p:
        p["errordef"] = 1.
      #m = iminuit.Minuit(self,print_level=0,pedantic=False,**p)
      m = iminuit.Minuit(self,**p)
      if showInit:
        model = self.model(*m.args)
        plt.figure("initial pars")
        plt.grid()
        plt.plot(self.x,self.data,"o")
        plt.plot(self.x,model,'r-',linewidth=2)
        raw_input()
      if doFit:
        m.migrad()
        if doMinos:
          m.minos()
          for p in m.parameters:
            err = m.get_merrors()[p]
            err = "+ %.4f - %.4f" % (np.abs(err["upper"]),np.abs(err["lower"]))
            print("%10s %.4f %s"%(p,m.values[p],err))
        else:
          for p in m.parameters:
            err = m.errors[p]
            err = "+/- %.4f" % (err)
            print("%10s %.4f %s"%(p,m.values[p],err))

      model = self.model(*m.args)
      if (showPlot):
        plt.figure("final fit")
        plt.grid()
        plt.plot(self.x,self.data,"o")
        plt.plot(self.x,model,'r-',linewidth=2)
      self.m = m
      return m,self.x,self.data,model

  return iminuitFit


def iminuitParsToStr(iminuit,withErrs=True,withFixed=True):
  values = iminuit.values
  errs   = iminuit.errors
  pnames = values.keys()
  lenParNames = max( [len(p) for p in pnames] )
  fmt = "%%%ds" % lenParNames
  pnames.sort()
  res = []
  for p in pnames:
    v = values[p]
    e = errs[p]
    isf = iminuit.is_fixed(p)
    if not withFixed and isf:
      continue
    v,e = approx_err(v,e,asstring=True)
    if isf: e="fixed"
    s  = fmt % p
    if withErrs:
      s += " = %s +/- %s" % (v,e)
    else:
      s += " = %s" % (v)
    res.append(s)
  return res


### VARIOUS ###

def myProgressBar(N,title="Percentage"):
  import progressbar as pb
  widgets = [title, pb.Percentage(), ' ', pb.Bar(), ' ', pb.ETA()]
  pbar = pb.ProgressBar(widgets=widgets, maxval=N)
  return pbar

def chunk(iterableOrNum, size):
  temp = []
  try:
    n = len(iterableOrNum)
  except TypeError:
    n = iterableOrNum
  nGroups = int(np.ceil(float(n)/size))
  for i in range(nGroups):
    m = i*size
    M = (i+1)*size; M=min(M,n)
    if (m>=n):
      break
    temp.append( slice(m,M) )
  try:
    ret = [iterableOrNum[x] for x in temp]
  except TypeError:
    ret = temp
  return ret

def timeres(*K):
  """ return sqrt(a1**2+a2**2+...) """
  s = 0
  for k in K:
    s += k**2
  return np.sqrt(s)

def approx_err(value,err,asstring=False):
  if (not (np.isfinite(err))):
    err = np.abs(value/1e3)
  if (err != 0):
    ndigerr = -int(np.floor(np.log10(err)))
    if (ndigerr<1): ndigerr=2
    e =round(err,ndigerr)
    ndigerr = -int(np.floor(np.log10(err)))
    v =round(value,ndigerr)
  else:
    v=value
    e=err
  if (asstring):
    return "%s" % v,"%s" % e
  else:
    return v,e

def linFitOld(A,B):
  """ solve Ax = B, returning x """
  temp = np.dot(A.T,B)
  square = np.dot(A.T,A)
  if (np.asarray(square).ndim==0):
    inv = 1./square
  else:
    inv = np.linalg.inv(square)
  x = np.dot(inv,temp)
  return x



def linFit(A,B,cond=None):
  """ solve Ax = B, returning x """
  from scipy import linalg
  temp = np.dot(A.T,B)
  square = np.dot(A.T,A)
  if (np.asarray(square).ndim==0):
    inv = 1./square
  else:
    inv = linalg.pinvh(square,cond=cond)
  x = np.dot(inv,temp)
  return x
  #return np.linalg.lstsq(A,B)[0]

def insertInSortedArray(a,v):
  if v>a.max(): return a
  idx = np.argmin(a<v)
  # move to the right the values bigger than v
  a[idx+1:] = a[idx:-1]
  a[idx]=v
  return a


### Objects ###

class dropObject(object):
  pass

  def __getitem__(self,x):
    return self.__dict__[x]

  def __setitem__(self,x,v):
    self.__dict__[x] = v

  def _add(self,name,data):
    self.__dict__[name]=data

  def __str__(self):
    return "dropObject with keys %s" % self.keys()

  def keys(self):
    k = self.__dict__.keys()
    k.sort()
    return k

  def __repr__(self):
    return self.__str__()


def dict2class(d,recursive=True,cleanNames=True):
  """Return a class that has same attributes/values and 
     dictionaries key/value
  """
  #see if it is indeed a dictionary
  if type(d) != types.DictType:
      return None
  
  #define a dummy class
  c = dropObject()
  for elem in d.keys():
      key = elem
      if cleanNames:
        try:
          int(elem)
          key = "value%s" % elem
        except:
          pass
      if recursive and (type(d[elem]) == types.DictType):
        c.__dict__[key] = dict2class(d[elem])
      else:
        c.__dict__[key] = d[elem]
  return c

def Hdf5ToObj(h5):
  import h5py
  if isinstance(h5,h5py.File) or isinstance(h5,h5py.Group):
    h5hande = h5
  else:
    h5hande = h5py.File(h5,"r")
  ret = dropObject()
  for h in h5hande:
    name = h.replace(":","_")
    name = name.replace(".","_")
    if not isinstance(h5hande[h],h5py.Dataset):
      ret._add(name,Hdf5ToObj(h5hande[h]))
    else:
      ret._add(name,h5hande[h])
  return ret


def fac(n):
  import math
#  http://rosettacode.org/wiki/Prime_decomposition#Python
  step = lambda x: 1 + x*4 - (x/2)*2
  maxq = long(math.floor(math.sqrt(n)))
  d = 1
  q = n % 2 == 0 and 2 or 3 
  while q <= maxq and n % q != 0:
    q = step(d)
    d += 1
  res = []
  if q <= maxq:
     res.extend(fac(n//q))
     res.extend(fac(q)) 
  else: res=[n]
  return res



def define_colors(fname="colorbrewer_all_schemes.json"):
  if not os.path.exists(fname):
    fname = os.path.dirname(os.path.realpath(__file__)) + "/" + fname
  if not os.path.exists(fname):
    print("Cannot find colorbrewer_all_schemes.json can't continue")
    print(fname)
    return
  if globals()["colors"] is None:
    import json
    ff = open(fname,"r")
    f = json.load( ff )
    ff.close()
    colors = dict2class(f)
    for t1 in colors.keys():
      for seq in colors[t1].keys():
        for nc in colors[t1][seq].keys():
          colors[t1][seq][nc] = np.asarray(colors[t1][seq][nc]["Colors"])/255.
    globals()["colors"] = colors

def colors_example_nature(nature,title="colors"):
  import pylab as plt
  x = np.arange(10)
  schemes = nature.keys()
  nSchemes = len(schemes)
  nSequenceMax = max( [len(nature[s].keys()) for s in schemes] )
  fig,ax = plt.subplots(nSchemes,nSequenceMax,
          sharex=True,sharey=True,num=title)
  for nScheme in range(nSchemes):
    scheme    = nature[schemes[nScheme]]
    sequences = scheme.keys()
    nSequences = len(sequences)
    for i in range(nSequences):
      mycolors = nature[schemes[nScheme]][sequences[i]]
      for j,c in enumerate(mycolors):
        ax[nScheme][i].axhline(j,color=c)
      ax[nScheme][i].set_title("%s %s" % (schemes[nScheme],sequences[i]))
  
def colors_example():
  define_colors()
  for nature in colors.keys():
    colors_example_nature(colors[nature],nature)

try:
  define_colors()
except:
  pass