more verbose description
This commit is contained in:
Martin Diehl
parent
251d55fe09
commit
9beca6488c
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@ -1,5 +1,3 @@
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from fractions import Fraction
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from functools import reduce
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from queue import Queue
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import re
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import glob
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@ -13,6 +11,7 @@ import numpy as np
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from . import util
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from . import version
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from . import mechanics
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from . import Rotation
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from . import Orientation
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from . import Environment
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@ -282,7 +281,7 @@ class DADF5():
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def del_visible(self,what,datasets):
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"""
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Delete from active groupse.
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Delete from active groupe.
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Parameters
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----------
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@ -661,7 +660,7 @@ class DADF5():
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self.__add_generic_pointwise(__add_eigenvector,requested)
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def add_IPFcolor(self,q,p=[0,0,1]):
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def add_IPFcolor(self,q,p):
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"""
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Add RGB color tuple of inverse pole figure (IPF) color.
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@ -670,51 +669,36 @@ class DADF5():
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q : str
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Label of the dataset containing the orientation data as quaternions.
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p : list of int
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Pole direction as Miller indices. Default value is [0, 0, 1].
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Pole direction as Miller indices.
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"""
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def __add_IPFcolor(orientation,pole):
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def __add_IPFcolor(q,p):
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MAX_DENOMINATOR = 1000
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def lcm(a, b):
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"""Least common multiple."""
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return a * b // np.gcd(a, b)
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def get_square_denominator(x):
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"""returns the denominator of the square of a number."""
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return Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
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def scale_to_Miller(v):
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"""Factor to scale vector to integers."""
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denominators = [int(get_square_denominator(i)) for i in v]
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s = reduce(lcm, denominators) ** 0.5
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m = (np.array(v)*s).astype(np.int)
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return m//reduce(np.gcd,m)
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m = scale_to_Miller(pole)
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lattice = orientation['meta']['Lattice']
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pole = np.array(p)
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unit_pole = pole/np.linalg.norm(pole)
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colors = np.empty((len(orientation['data']),3),np.uint8)
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m = util.scale_to_coprime(pole)
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colors = np.empty((len(q['data']),3),np.uint8)
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for i,q in enumerate(orientation['data']):
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lattice = q['meta']['Lattice']
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for i,q in enumerate(q['data']):
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o = Orientation(np.array([q['w'],q['x'],q['y'],q['z']]),lattice).reduced()
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colors[i] = np.uint8(o.IPFcolor(unit_pole)*255)
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colors[i] = np.uint8(o.IPFcolor(unit_pole)*255)
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return {
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'data': colors,
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'label': 'IPFcolor_[{} {} {}]'.format(*m),
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'label': 'IPFcolor_{{{} {} {}>'.format(*m),
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'meta' : {
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'Unit': 'RGB (8bit)',
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'Lattice': lattice,
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'Description': 'Inverse Pole Figure colors',
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'Description': 'Inverse Pole Figure (IPF) colors for direction/plane [{} {} {})'.format(*m),
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'Creator': 'dadf5.py:addIPFcolor v{}'.format(version)
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}
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}
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requested = [{'label':q,'arg':'orientation'}]
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requested = [{'label':q,'arg':'q'}]
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self.__add_generic_pointwise(__add_IPFcolor,requested,{'pole':p})
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self.__add_generic_pointwise(__add_IPFcolor,requested,{'p':p})
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def add_maximum_shear(self,x):
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@ -846,49 +830,47 @@ class DADF5():
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self.__add_generic_pointwise(__add_PK2,requested)
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def addPole(self,q,p,polar=False):
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def add_pole(self,q,p,polar=False):
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"""
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Add coordinates of stereographic projection of given direction (pole) in crystal frame.
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Add coordinates of stereographic projection of given pole in crystal frame.
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Parameters
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----------
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q : str
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Label of the dataset containing the crystallographic orientation as a quaternion.
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p : numpy.array of shape (3)
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Pole (direction) in crystal frame.
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Pole in crystal frame.
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polar : bool, optional
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Give pole in polar coordinates. Default is false.
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"""
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def __addPole(orientation,pole):
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def __add_pole(q,p,polar):
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pole = np.array(pole)
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unit_pole /= np.linalg.norm(pole)
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coords = np.empty((len(orientation['data']),2))
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pole = np.array(p)
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unit_pole = pole/np.linalg.norm(pole)
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m = util.scale_to_coprime(pole)
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coords = np.empty((len(q['data']),2))
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for i,q in enumerate(orientation['data']):
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for i,q in enumerate(q['data']):
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o = Rotation(np.array([q['w'],q['x'],q['y'],q['z']]))
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rotatedPole = o*pole # rotate pole according to crystal orientation
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(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
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if polar is True:
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coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)]
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else:
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coords[i] = [x,y]
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coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y]
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return {
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'data': coords,
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'label': 'Pole',
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'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
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'meta' : {
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'Unit': '1',
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'Description': 'Coordinates of stereographic projection of given direction (pole) in crystal frame',
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'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
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.format('Polar' if polar else 'Cartesian'),
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'Creator' : 'dadf5.py:addPole v{}'.format(version)
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}
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}
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requested = [{'label':'orientation','arg':'orientation'}]
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requested = [{'label':q,'arg':'q'}]
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self.__add_generic_pointwise(__addPole,requested,{'pole':pole})
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self.__add_generic_pointwise(__add_pole,requested,{'p':p,'polar':polar})
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def add_rotational_part(self,F='F'):
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@ -3,14 +3,18 @@ import time
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import os
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import subprocess
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import shlex
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from fractions import Fraction
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from functools import reduce
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from optparse import Option
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from queue import Queue
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from threading import Thread
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import numpy as np
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class bcolors:
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"""
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ASCII Colors (Blender code).
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https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
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http://stackoverflow.com/questions/287871/print-in-terminal-with-colors-using-python
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"""
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@ -36,7 +40,7 @@ class bcolors:
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self.BOLD = ''
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self.UNDERLINE = ''
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self.CROSSOUT = ''
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# -----------------------------
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def srepr(arg,glue = '\n'):
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@ -159,11 +163,30 @@ def progressBar(iteration, total, prefix='', bar_length=50):
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if iteration == total: sys.stderr.write('\n')
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sys.stderr.flush()
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def scale_to_coprime(v):
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"""Scale vector to co-prime (relatively prime) integers."""
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MAX_DENOMINATOR = 1000
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def get_square_denominator(x):
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"""returns the denominator of the square of a number."""
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return Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
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def lcm(a, b):
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"""Least common multiple."""
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return a * b // np.gcd(a, b)
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denominators = [int(get_square_denominator(i)) for i in v]
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s = reduce(lcm, denominators) ** 0.5
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m = (np.array(v)*s).astype(np.int)
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return m//reduce(np.gcd,m)
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class return_message():
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"""Object with formatted return message."""
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def __init__(self,message):
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"""
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Sets return message.
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@ -175,7 +198,7 @@ class return_message():
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"""
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self.message = message
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def __repr__(self):
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"""Return message suitable for interactive shells."""
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return srepr(self.message)
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