DAMASK_EICMD/lib/damask/util.py

# -*- coding: UTF-8 no BOM -*-
import sys,time,random,threading,os,subprocess,shlex
import numpy as np
from optparse import Option

class bcolors:
    """
    ASCII Colors (Blender code)
    
    https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
    http://stackoverflow.com/questions/287871/print-in-terminal-with-colors-using-python
    """

    HEADER = '\033[95m'
    OKBLUE = '\033[94m'
    OKGREEN = '\033[92m'
    WARNING = '\033[93m'
    FAIL = '\033[91m'
    ENDC = '\033[0m'
    BOLD = '\033[1m'
    DIM  = '\033[2m'
    UNDERLINE = '\033[4m'

    def disable(self):
        self.HEADER = ''
        self.OKBLUE = ''
        self.OKGREEN = ''
        self.WARNING = ''
        self.FAIL = ''
        self.ENDC = ''
        self.BOLD = ''
        self.UNDERLINE = ''
    

# -----------------------------
def srepr(arg,glue = '\n'):
  """Joins arguments as individual lines"""
  if (not hasattr(arg, "strip") and
          (hasattr(arg, "__getitem__") or
           hasattr(arg, "__iter__"))):
     return glue.join(str(x) for x in arg)
  return arg if isinstance(arg,str) else repr(arg)

# -----------------------------
def croak(what, newline = True):
  """Writes formated to stderr"""
  sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
  sys.stderr.flush()

# -----------------------------
def report(who = None,
           what = None):
  """Reports script and file name"""
  croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') )


# -----------------------------
def report_geom(info,
                what = ['grid','size','origin','homogenization','microstructures']):
  """Reports (selected) geometry information"""
  output = {
            'grid'   : 'grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'  ])))),
            'size'   : 'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'  ])))),
            'origin' : 'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
            'homogenization' :  'homogenization:  {}'.format(info['homogenization']),
            'microstructures' : 'microstructures: {}'.format(info['microstructures']),
           }
  for item in what: croak(output[item.lower()])

# -----------------------------
def emph(what):
  """Boldens string"""
  return bcolors.BOLD+srepr(what)+bcolors.ENDC

# -----------------------------
def deemph(what):
  """Dims string"""
  return bcolors.DIM+srepr(what)+bcolors.ENDC

# -----------------------------
def delete(what):
  """Dims string"""
  return bcolors.DIM+srepr(what)+bcolors.ENDC

# -----------------------------
def execute(cmd,
            streamIn = None,
            wd = './'):
  """Executes a command in given directory and returns stdout and stderr for optional stdin"""
  initialPath = os.getcwd()
  os.chdir(wd)
  process = subprocess.Popen(shlex.split(cmd),
                             stdout = subprocess.PIPE,
                             stderr = subprocess.PIPE,
                             stdin  = subprocess.PIPE)
  out,error = [i for i in (process.communicate() if streamIn is None
                                                 else process.communicate(streamIn.read().encode('utf-8')))]
  out   = out.decode('utf-8').replace('\x08','')
  error = error.decode('utf-8').replace('\x08','')
  os.chdir(initialPath)
  if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
  return out,error

def coordGridAndSize(coordinates):
  """Determines grid count and overall physical size along each dimension of an ordered array of coordinates"""
  dim    = coordinates.shape[1]
  coords = [np.unique(coordinates[:,i]) for i in range(dim)]
  mincorner = np.array(list(map(min,coords)))
  maxcorner = np.array(list(map(max,coords)))
  grid   = np.array(list(map(len,coords)),'i')
  size   = grid/np.maximum(np.ones(dim,'d'), grid-1.0) * (maxcorner-mincorner)                      # size from edge to edge = dim * n/(n-1) 
  size   = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1]))                             # spacing for grid==1 equal to smallest among other ones
  return grid,size
  
# -----------------------------
class extendableOption(Option):
  """
  Used for definition of new option parser action 'extend', which enables to take multiple option arguments

  taken from online tutorial http://docs.python.org/library/optparse.html
  """

  ACTIONS = Option.ACTIONS + ("extend",)
  STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
  TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
  ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)

  def take_action(self, action, dest, opt, value, values, parser):
    if action == "extend":
      lvalue = value.split(",")
      values.ensure_value(dest, []).extend(lvalue)
    else:
      Option.take_action(self, action, dest, opt, value, values, parser)

# -----------------------------
class backgroundMessage(threading.Thread):
  """Reporting with animation to indicate progress"""

  choices = {'bounce':   ['_', 'o', 'O', '°', '‾', '‾', '°', 'O', 'o', '_'],
             'spin':     ['◜', '◝', '◞', '◟'],
             'circle':   ['◴', '◵', '◶', '◷'],
             'hexagon':  ['⬢', '⬣'],
             'square':   ['▖', '▘', '▝', '▗'],
             'triangle': ['ᐊ', 'ᐊ', 'ᐃ', 'ᐅ', 'ᐅ', 'ᐃ'],
             'amoeba':   ['▖', '▏', '▘', '▔', '▝', '▕', '▗', '▁'],
             'beat':     ['▁', '▂', '▃', '▅', '▆', '▇', '▇', '▆', '▅', '▃', '▂'],
             'prison':   ['ᚋ', 'ᚌ', 'ᚍ', 'ᚏ', 'ᚎ', 'ᚍ', 'ᚌ', 'ᚋ'],
             'breath':   ['ᚐ', 'ᚑ', 'ᚒ', 'ᚓ', 'ᚔ', 'ᚓ', 'ᚒ', 'ᚑ', 'ᚐ'],
             'pulse':    ['·', '•', '●', '●', '•'],
             'ant':      ['⠁', '⠂', '⠐', '⠠', '⠄', '⡀', '⢀', '⠠', '⠄', '⠂', '⠐', '⠈'],
             'juggle':   ['꜈', '꜉', '꜊', '꜋', '꜌', '꜑', '꜐', '꜏', '꜍'],
#             'wobbler':  ['▁', '◣', '▏', '◤', '▔', '◥', '▕', '◢'],
             'grout':    ['▁', '▏', '▔', '▕'],
             'partner':  ['⚬', '⚭', '⚮', '⚯', '⚮', '⚭'],
             'classic':  ['-', '\\', '|', '/',],
            }    

  def __init__(self,symbol = None,wait = 0.1):
    """Sets animation symbol"""
    super(backgroundMessage, self).__init__()
    self._stop = threading.Event()
    self.message = ''
    self.new_message = ''
    self.counter = 0
    self.gap     = ' '
    self.symbols = self.choices[symbol if symbol in self.choices else random.choice(list(self.choices.keys()))]
    self.waittime = wait
  
  def __quit__(self):
    """Cleans output"""
    length = len(self.symbols[self.counter] + self.gap + self.message)
    sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length)
    sys.stderr.write('')
    sys.stderr.flush()
  
  def stop(self):
    self._stop.set()

  def stopped(self):
    return self._stop.is_set()

  def run(self):
    while not threading.enumerate()[0]._Thread__stopped:
      time.sleep(self.waittime)
      self.update_message()
    self.__quit__()

  def set_message(self, new_message):
    self.new_message = new_message
    self.print_message()
  
  def print_message(self):
    length = len(self.symbols[self.counter] + self.gap + self.message)
    sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length + \
                     self.symbols[self.counter] + self.gap + self.new_message)      # delete former and print new message
    sys.stderr.flush()
    self.message = self.new_message
      
  def update_message(self):
    self.counter = (self.counter + 1)%len(self.symbols)
    self.print_message()

  def animation(self,which = None):
    return ''.join(self.choices[which]) if which in self.choices else ''


def leastsqBound(func, x0, args=(), bounds=None, Dfun=None, full_output=0,
                col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8,
                gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None):
  from scipy.optimize import _minpack
  """
  Non-linear least square fitting (Levenberg-Marquardt method) with 
  bounded parameters.
  the codes of transformation between int <-> ext refers to the work of
  Jonathan J. Helmus: https://github.com/jjhelmus/leastsqbound-scipy
  other codes refers to the source code of minpack.py:
  ..\Lib\site-packages\scipy\optimize\minpack.py

  An internal parameter list is used to enforce contraints on the fitting 
  parameters. The transfomation is based on that of MINUIT package. 
  please see: F. James and M. Winkler. MINUIT User's Guide, 2004.

  bounds : list
    (min, max) pairs for each parameter, use None for 'min' or 'max' 
    when there is no bound in that direction. 
    For example: if there are two parameters needed to be fitting, then
    bounds is [(min1,max1), (min2,max2)]
    
  This function is based on 'leastsq' of minpack.py, the annotation of
  other parameters can be found in 'leastsq'.
  ..\Lib\site-packages\scipy\optimize\minpack.py
  """
 
  def _check_func(checker, argname, thefunc, x0, args, numinputs,
                output_shape=None):
    from numpy import shape
    """The same as that of minpack.py"""
    res = np.atleast_1d(thefunc(*((x0[:numinputs],) + args)))
    if (output_shape is not None) and (shape(res) != output_shape):
        if (output_shape[0] != 1):
            if len(output_shape) > 1:
                if output_shape[1] == 1:
                    return shape(res)
            msg = "%s: there is a mismatch between the input and output " \
                  "shape of the '%s' argument" % (checker, argname)
            func_name = getattr(thefunc, '__name__', None)
            if func_name:
                msg += " '%s'." % func_name
            else:
                msg += "."
            raise TypeError(msg)
    if np.issubdtype(res.dtype, np.inexact):
        dt = res.dtype
    else:
        dt = dtype(float)
    return shape(res), dt
  
  def _int2extGrad(p_int, bounds):
    """Calculate the gradients of transforming the internal (unconstrained) to external (constrained) parameter."""
    grad = np.empty_like(p_int)
    for i, (x, bound) in enumerate(zip(p_int, bounds)):
        lower, upper = bound
        if lower is None and upper is None:  # No constraints
            grad[i] = 1.0
        elif upper is None:                  # only lower bound
            grad[i] =  x/np.sqrt(x*x + 1.0)
        elif lower is None:                  # only upper bound
            grad[i] = -x/np.sqrt(x*x + 1.0)
        else:                                # lower and upper bounds
            grad[i] = (upper - lower)*np.cos(x)/2.0
    return grad
  
  def _int2extFunc(bounds):
    """Transform internal parameters into external parameters."""
    local = [_int2extLocal(b) for b in bounds]
    def _transform_i2e(p_int):
        p_ext = np.empty_like(p_int)
        p_ext[:] = [i(j) for i, j in zip(local, p_int)]
        return p_ext
    return _transform_i2e
  
  def _ext2intFunc(bounds):
    """Transform external parameters into internal parameters."""
    local = [_ext2intLocal(b) for b in bounds]
    def _transform_e2i(p_ext):
        p_int = np.empty_like(p_ext)
        p_int[:] = [i(j) for i, j in zip(local, p_ext)]
        return p_int
    return _transform_e2i

  def _int2extLocal(bound):
    """Transform a single internal parameter to an external parameter."""
    lower, upper = bound
    if lower is None and upper is None:      # no constraints
        return lambda x: x
    elif upper is None:                      # only lower bound
        return lambda x: lower - 1.0 + np.sqrt(x*x + 1.0)
    elif lower is None:                      # only upper bound
        return lambda x: upper + 1.0 - np.sqrt(x*x + 1.0)
    else:
        return lambda x: lower + ((upper - lower)/2.0)*(np.sin(x) + 1.0)
  
  def _ext2intLocal(bound):
    """Transform a single external parameter to an internal parameter."""
    lower, upper = bound
    if lower is None and upper is None:  # no constraints
        return lambda x: x
    elif upper is None:                  # only lower bound
        return lambda x: np.sqrt((x - lower + 1.0)**2 - 1.0)
    elif lower is None:                  # only upper bound
        return lambda x: np.sqrt((x - upper - 1.0)**2 - 1.0)
    else:
        return lambda x: np.arcsin((2.0*(x - lower)/(upper - lower)) - 1.0)
  
  i2e = _int2extFunc(bounds)
  e2i = _ext2intFunc(bounds)
  
  x0 = np.asarray(x0).flatten()
  n = len(x0)

  if len(bounds) != n:
      raise ValueError('the length of bounds is inconsistent with the number of parameters ')
  
  if not isinstance(args, tuple):
      args = (args,)
  
  shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
  m = shape[0]

  if n > m:
      raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
  if epsfcn is None:
      epsfcn = np.finfo(dtype).eps

  def funcWarp(x, *args):
      return func(i2e(x), *args)

  xi0 = e2i(x0)
  
  if Dfun is None:
      if maxfev == 0:
          maxfev = 200*(n + 1)
      retval = _minpack._lmdif(funcWarp, xi0, args, full_output, ftol, xtol,
                               gtol, maxfev, epsfcn, factor, diag)
  else:
      if col_deriv:
          _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
      else:
          _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
      if maxfev == 0:
          maxfev = 100*(n + 1)

      def DfunWarp(x, *args):
          return Dfun(i2e(x), *args)

      retval = _minpack._lmder(funcWarp, DfunWarp, xi0, args, full_output, col_deriv,
                               ftol, xtol, gtol, maxfev, factor, diag)

  errors = {0: ["Improper input parameters.", TypeError],
            1: ["Both actual and predicted relative reductions "
                "in the sum of squares\n  are at most %f" % ftol, None],
            2: ["The relative error between two consecutive "
                "iterates is at most %f" % xtol, None],
            3: ["Both actual and predicted relative reductions in "
                "the sum of squares\n  are at most %f and the "
                "relative error between two consecutive "
                "iterates is at \n  most %f" % (ftol, xtol), None],
            4: ["The cosine of the angle between func(x) and any "
                "column of the\n  Jacobian is at most %f in "
                "absolute value" % gtol, None],
            5: ["Number of calls to function has reached "
                "maxfev = %d." % maxfev, ValueError],
            6: ["ftol=%f is too small, no further reduction "
                "in the sum of squares\n  is possible.""" % ftol,
                ValueError],
            7: ["xtol=%f is too small, no further improvement in "
                "the approximate\n  solution is possible." % xtol,
                ValueError],
            8: ["gtol=%f is too small, func(x) is orthogonal to the "
                "columns of\n  the Jacobian to machine "
                "precision." % gtol, ValueError],
            'unknown': ["Unknown error.", TypeError]}

  info = retval[-1]    # The FORTRAN return value
  
  if info not in [1, 2, 3, 4] and not full_output:
      if info in [5, 6, 7, 8]:
          np.warnings.warn(errors[info][0], RuntimeWarning)
      else:
          try:
              raise errors[info][1](errors[info][0])
          except KeyError:
              raise errors['unknown'][1](errors['unknown'][0])

  mesg = errors[info][0]
  x = i2e(retval[0])

  if full_output:
      grad = _int2extGrad(retval[0], bounds)
      retval[1]['fjac'] = (retval[1]['fjac'].T / np.take(grad,
                           retval[1]['ipvt'] - 1)).T
      cov_x = None
      if info in [1, 2, 3, 4]:
          from numpy.dual import inv
          from numpy.linalg import LinAlgError
          perm = np.take(np.eye(n), retval[1]['ipvt'] - 1, 0)
          r = np.triu(np.transpose(retval[1]['fjac'])[:n, :])
          R = np.dot(r, perm)
          try:
              cov_x = inv(np.dot(np.transpose(R), R))
          except LinAlgError as inverror:
              print(inverror)
              pass
      return (x, cov_x) + retval[1:-1] + (mesg, info)
  else:
      return (x, info)

def _general_function(params, ydata, xdata, function):
    return  function(xdata, *params) - ydata
def _weighted_general_function(params, ydata, xdata, function, weights):
    return (function(xdata, *params) - ydata)*weights

def curve_fit_bound(f, xdata, ydata, p0=None, sigma=None, bounds=None, **kw):
    """Similar as 'curve_fit' in minpack.py"""
    if p0 is None:
        # determine number of parameters by inspecting the function
        import inspect
        args, varargs, varkw, defaults = inspect.getargspec(f)
        if len(args) < 2:
            msg = "Unable to determine number of fit parameters."
            raise ValueError(msg)
        if 'self' in args:
            p0 = [1.0] * (len(args)-2)
        else:
            p0 = [1.0] * (len(args)-1)

    if np.isscalar(p0):
        p0 = np.array([p0])

    args = (ydata, xdata, f)
    if sigma is None:
        func = _general_function
    else:
        func = _weighted_general_function
        args += (1.0/np.asarray(sigma),)

    return_full = kw.pop('full_output', False)
    res = leastsqBound(func, p0, args=args, bounds = bounds, full_output=True, **kw)
    (popt, pcov, infodict, errmsg, ier) = res

    if ier not in [1, 2, 3, 4]:
        msg = "Optimal parameters not found: " + errmsg
        raise RuntimeError(msg)

    if (len(ydata) > len(p0)) and pcov is not None:
        s_sq = (func(popt, *args)**2).sum()/(len(ydata)-len(p0))
        pcov = pcov * s_sq
    else:
        pcov = np.inf

    return (popt, pcov, infodict, errmsg, ier) if return_full else (popt, pcov)