1176 lines
42 KiB
Python
1176 lines
42 KiB
Python
from queue import Queue
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import re
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import glob
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import os
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import vtk
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from vtk.util import numpy_support
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import h5py
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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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from . import grid_filters
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class DADF5():
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"""
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Read and write to DADF5 files.
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DADF5 files contain DAMASK results.
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"""
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def __init__(self,fname):
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"""
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Opens an existing DADF5 file.
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Parameters
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----------
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fname : str
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name of the DADF5 file to be openend.
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"""
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with h5py.File(fname,'r') as f:
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try:
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self.version_major = f.attrs['DADF5_version_major']
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self.version_minor = f.attrs['DADF5_version_minor']
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except KeyError:
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self.version_major = f.attrs['DADF5-major']
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self.version_minor = f.attrs['DADF5-minor']
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if self.version_major != 0 or not 2 <= self.version_minor <= 6:
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raise TypeError('Unsupported DADF5 version {}.{} '.format(f.attrs['DADF5_version_major'],
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f.attrs['DADF5_version_minor']))
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self.structured = 'grid' in f['geometry'].attrs.keys()
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if self.structured:
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self.grid = f['geometry'].attrs['grid']
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self.size = f['geometry'].attrs['size']
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if self.version_major == 0 and self.version_minor >= 5:
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self.origin = f['geometry'].attrs['origin']
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r=re.compile('inc[0-9]+')
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increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)}
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self.increments = [increments_unsorted[i] for i in sorted(increments_unsorted)]
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self.times = [round(f[i].attrs['time/s'],12) for i in self.increments]
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self.Nmaterialpoints, self.Nconstituents = np.shape(f['mapping/cellResults/constituent'])
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self.materialpoints = [m.decode() for m in np.unique(f['mapping/cellResults/materialpoint']['Name'])]
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self.constituents = [c.decode() for c in np.unique(f['mapping/cellResults/constituent'] ['Name'])]
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self.con_physics = []
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for c in self.constituents:
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self.con_physics += f['/'.join([self.increments[0],'constituent',c])].keys()
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self.con_physics = list(set(self.con_physics)) # make unique
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self.mat_physics = []
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for m in self.materialpoints:
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self.mat_physics += f['/'.join([self.increments[0],'materialpoint',m])].keys()
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self.mat_physics = list(set(self.mat_physics)) # make unique
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self.selection= {'increments': self.increments,
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'constituents': self.constituents,
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'materialpoints': self.materialpoints,
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'con_physics': self.con_physics,
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'mat_physics': self.mat_physics}
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self.fname = fname
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def __manage_visible(self,datasets,what,action):
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"""
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Manages the visibility of the groups.
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Parameters
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----------
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datasets : list of str or Boolean
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name of datasets as list, supports ? and * wildcards.
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True is equivalent to [*], False is equivalent to []
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what : str
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attribute to change (must be in self.selection)
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action : str
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select from 'set', 'add', and 'del'
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"""
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# allow True/False and string arguments
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if datasets is True:
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datasets = ['*']
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elif datasets is False:
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datasets = []
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choice = [datasets] if isinstance(datasets,str) else datasets
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valid = [e for e_ in [glob.fnmatch.filter(getattr(self,what),s) for s in choice] for e in e_]
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existing = set(self.selection[what])
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if action == 'set':
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self.selection[what] = valid
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elif action == 'add':
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add=existing.union(valid)
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add_sorted=sorted(add, key=lambda x: int("".join([i for i in x if i.isdigit()])))
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self.selection[what] = add_sorted
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elif action == 'del':
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diff=existing.difference(valid)
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diff_sorted=sorted(diff, key=lambda x: int("".join([i for i in x if i.isdigit()])))
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self.selection[what] = diff_sorted
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def __time_to_inc(self,start,end):
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selected = []
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for i,time in enumerate(self.times):
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if start <= time <= end:
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selected.append(self.increments[i])
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return selected
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def set_by_time(self,start,end):
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"""
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Set active increments based on start and end time.
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Parameters
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----------
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start : float
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start time (included)
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end : float
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end time (included)
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"""
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self.__manage_visible(self.__time_to_inc(start,end),'increments','set')
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def add_by_time(self,start,end):
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"""
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Add to active increments based on start and end time.
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Parameters
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----------
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start : float
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start time (included)
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end : float
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end time (included)
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"""
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self.__manage_visible(self.__time_to_inc(start,end),'increments','add')
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def del_by_time(self,start,end):
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"""
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Delete from active increments based on start and end time.
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Parameters
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----------
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start : float
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start time (included)
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end : float
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end time (included)
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"""
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self.__manage_visible(self.__time_to_inc(start,end),'increments','del')
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def set_by_increment(self,start,end):
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"""
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Set active time increments based on start and end increment.
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Parameters
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----------
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start : int
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start increment (included)
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end : int
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end increment (included)
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"""
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if self.version_minor >= 4:
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self.__manage_visible([ 'inc{}'.format(i) for i in range(start,end+1)],'increments','set')
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else:
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self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','set')
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def add_by_increment(self,start,end):
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"""
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Add to active time increments based on start and end increment.
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Parameters
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----------
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start : int
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start increment (included)
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end : int
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end increment (included)
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"""
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if self.version_minor >= 4:
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self.__manage_visible([ 'inc{}'.format(i) for i in range(start,end+1)],'increments','add')
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else:
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self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','add')
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def del_by_increment(self,start,end):
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"""
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Delet from active time increments based on start and end increment.
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Parameters
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----------
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start : int
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start increment (included)
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end : int
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end increment (included)
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"""
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if self.version_minor >= 4:
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self.__manage_visible([ 'inc{}'.format(i) for i in range(start,end+1)],'increments','del')
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else:
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self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','del')
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def iter_visible(self,what):
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"""
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Iterate over visible items by setting each one visible.
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Parameters
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----------
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what : str
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attribute to change (must be in self.selection)
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"""
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datasets = self.selection[what]
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last_datasets = datasets.copy()
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for dataset in datasets:
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if last_datasets != self.selection[what]:
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self.__manage_visible(datasets,what,'set')
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raise Exception
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self.__manage_visible(dataset,what,'set')
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last_datasets = self.selection[what]
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yield dataset
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self.__manage_visible(datasets,what,'set')
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def set_visible(self,what,datasets):
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"""
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Set active groups.
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Parameters
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----------
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datasets : list of str or Boolean
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name of datasets as list, supports ? and * wildcards.
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True is equivalent to [*], False is equivalent to []
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what : str
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attribute to change (must be in self.selection)
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"""
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self.__manage_visible(datasets,what,'set')
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def add_visible(self,what,datasets):
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"""
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Add to active groups.
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Parameters
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----------
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datasets : list of str or Boolean
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name of datasets as list, supports ? and * wildcards.
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True is equivalent to [*], False is equivalent to []
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what : str
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attribute to change (must be in self.selection)
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"""
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self.__manage_visible(datasets,what,'add')
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def del_visible(self,what,datasets):
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"""
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Delete from active groupe.
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Parameters
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----------
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datasets : list of str or Boolean
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name of datasets as list, supports ? and * wildcards.
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True is equivalent to [*], False is equivalent to []
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what : str
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attribute to change (must be in self.selection)
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"""
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self.__manage_visible(datasets,what,'del')
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def groups_with_datasets(self,datasets):
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"""
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Get groups that contain all requested datasets.
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Only groups within inc?????/constituent/*_*/* inc?????/materialpoint/*_*/*
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are considered as they contain the data.
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Single strings will be treated as list with one entry.
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Wild card matching is allowed, but the number of arguments need to fit.
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Parameters
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----------
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datasets : iterable or str or boolean
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Examples
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--------
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datasets = False matches no group
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datasets = True matches all groups
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datasets = ['F','P'] matches a group with ['F','P','sigma']
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datasets = ['*','P'] matches a group with ['F','P']
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datasets = ['*'] does not match a group with ['F','P','sigma']
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datasets = ['*','*'] does not match a group with ['F','P','sigma']
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datasets = ['*','*','*'] matches a group with ['F','P','sigma']
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"""
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if datasets is False: return []
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sets = [datasets] if isinstance(datasets,str) else datasets
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groups = []
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with h5py.File(self.fname,'r') as f:
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for i in self.iter_visible('increments'):
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for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for oo in self.iter_visible(o):
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for pp in self.iter_visible(p):
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group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue
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if sets is True:
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groups.append(group)
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else:
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match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
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if len(set(match)) == len(sets) : groups.append(group)
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return groups
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def list_data(self):
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"""Return information on all active datasets in the file."""
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message = ''
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with h5py.File(self.fname,'r') as f:
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for i in self.iter_visible('increments'):
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message+='\n{} ({}s)\n'.format(i,self.times[self.increments.index(i)])
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for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for oo in self.iter_visible(o):
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message+=' {}\n'.format(oo)
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for pp in self.iter_visible(p):
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message+=' {}\n'.format(pp)
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group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue
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for d in f[group].keys():
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try:
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dataset = f['/'.join([group,d])]
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message+=' {} / ({}): {}\n'.\
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format(d,dataset.attrs['Unit'].decode(),dataset.attrs['Description'].decode())
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except KeyError:
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pass
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return message
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||
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def get_dataset_location(self,label):
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"""Return the location of all active datasets with given label."""
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path = []
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with h5py.File(self.fname,'r') as f:
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for i in self.iter_visible('increments'):
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k = '/'.join([i,'geometry',label])
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try:
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f[k]
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path.append(k)
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except KeyError as e:
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||
pass
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||
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for oo in self.iter_visible(o):
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||
for pp in self.iter_visible(p):
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k = '/'.join([i,o[:-1],oo,pp,label])
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try:
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f[k]
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path.append(k)
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except KeyError as e:
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pass
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return path
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||
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||
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def get_constituent_ID(self,c=0):
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||
"""Pointwise constituent ID."""
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with h5py.File(self.fname,'r') as f:
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names = f['/mapping/cellResults/constituent']['Name'][:,c].astype('str')
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return np.array([int(n.split('_')[0]) for n in names.tolist()],dtype=np.int32)
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||
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def get_crystal_structure(self): # ToDo: extension to multi constituents/phase
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"""Info about the crystal structure."""
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with h5py.File(self.fname,'r') as f:
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return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string
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||
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def read_dataset(self,path,c=0,plain=False):
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"""
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||
Dataset for all points/cells.
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||
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If more than one path is given, the dataset is composed of the individual contributions.
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"""
|
||
with h5py.File(self.fname,'r') as f:
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||
shape = (self.Nmaterialpoints,) + np.shape(f[path[0]])[1:]
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if len(shape) == 1: shape = shape +(1,)
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||
dataset = np.full(shape,np.nan,dtype=np.dtype(f[path[0]]))
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for pa in path:
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label = pa.split('/')[2]
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if (pa.split('/')[1] == 'geometry'):
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dataset = np.array(f[pa])
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continue
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p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
|
||
if len(p)>0:
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||
u = (f['mapping/cellResults/constituent']['Position'][p,c])
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||
a = np.array(f[pa])
|
||
if len(a.shape) == 1:
|
||
a=a.reshape([a.shape[0],1])
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||
dataset[p,:] = a[u,:]
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||
|
||
p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
|
||
if len(p)>0:
|
||
u = (f['mapping/cellResults/materialpoint']['Position'][p.tolist()])
|
||
a = np.array(f[pa])
|
||
if len(a.shape) == 1:
|
||
a=a.reshape([a.shape[0],1])
|
||
dataset[p,:] = a[u,:]
|
||
|
||
if plain and dataset.dtype.names is not None:
|
||
return dataset.view(('float64',len(dataset.dtype.names)))
|
||
else:
|
||
return dataset
|
||
|
||
|
||
def cell_coordinates(self):
|
||
"""Return initial coordinates of the cell centers."""
|
||
if self.structured:
|
||
return grid_filters.cell_coord0(self.grid,self.size,self.origin)
|
||
else:
|
||
with h5py.File(self.fname,'r') as f:
|
||
return f['geometry/x_c'][()]
|
||
|
||
|
||
def add_absolute(self,x):
|
||
"""
|
||
Add absolute value.
|
||
|
||
Parameters
|
||
----------
|
||
x : str
|
||
Label of scalar, vector, or tensor dataset to take absolute value of.
|
||
|
||
"""
|
||
def _add_absolute(x):
|
||
|
||
return {
|
||
'data': np.abs(x['data']),
|
||
'label': '|{}|'.format(x['label']),
|
||
'meta': {
|
||
'Unit': x['meta']['Unit'],
|
||
'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_abs v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_absolute,{'x':x})
|
||
|
||
|
||
def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True):
|
||
"""
|
||
Add result of a general formula.
|
||
|
||
Parameters
|
||
----------
|
||
label : str
|
||
Label of resulting dataset.
|
||
formula : str
|
||
Formula to calculate resulting dataset. Existing datasets are referenced by ‘#TheirLabel#‘.
|
||
unit : str, optional
|
||
Physical unit of the result.
|
||
description : str, optional
|
||
Human-readable description of the result.
|
||
vectorized : bool, optional
|
||
Indicate whether the formula can be used in vectorized form. Defaults to ‘True’.
|
||
|
||
"""
|
||
if not vectorized:
|
||
raise NotImplementedError
|
||
|
||
def _add_calculation(**kwargs):
|
||
|
||
formula = kwargs['formula']
|
||
for d in re.findall(r'#(.*?)#',formula):
|
||
formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
|
||
|
||
return {
|
||
'data': eval(formula),
|
||
'label': kwargs['label'],
|
||
'meta': {
|
||
'Unit': kwargs['unit'],
|
||
'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
|
||
'Creator': 'dadf5.py:add_calculation v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
|
||
args = {'formula':formula,'label':label,'unit':unit,'description':description}
|
||
|
||
self.__add_generic_pointwise(_add_calculation,dataset_mapping,args)
|
||
|
||
|
||
def add_Cauchy(self,P='P',F='F'):
|
||
"""
|
||
Add Cauchy stress calculated from first Piola-Kirchhoff stress and deformation gradient.
|
||
|
||
Parameters
|
||
----------
|
||
P : str, optional
|
||
Label of the dataset containing the first Piola-Kirchhoff stress. Defaults to ‘P’.
|
||
F : str, optional
|
||
Label of the dataset containing the deformation gradient. Defaults to ‘F’.
|
||
|
||
"""
|
||
def _add_Cauchy(P,F):
|
||
|
||
return {
|
||
'data': mechanics.Cauchy(P['data'],F['data']),
|
||
'label': 'sigma',
|
||
'meta': {
|
||
'Unit': P['meta']['Unit'],
|
||
'Description': 'Cauchy stress calculated from {} ({}) '.format(P['label'],
|
||
P['meta']['Description'])+\
|
||
'and {} ({})'.format(F['label'],F['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_Cauchy v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_Cauchy,{'P':P,'F':F})
|
||
|
||
|
||
def add_determinant(self,T):
|
||
"""
|
||
Add the determinant of a tensor.
|
||
|
||
Parameters
|
||
----------
|
||
T : str
|
||
Label of tensor dataset.
|
||
|
||
"""
|
||
def _add_determinant(T):
|
||
|
||
return {
|
||
'data': np.linalg.det(T['data']),
|
||
'label': 'det({})'.format(T['label']),
|
||
'meta': {
|
||
'Unit': T['meta']['Unit'],
|
||
'Description': 'Determinant of tensor {} ({})'.format(T['label'],T['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_determinant v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_determinant,{'T':T})
|
||
|
||
|
||
def add_deviator(self,T):
|
||
"""
|
||
Add the deviatoric part of a tensor.
|
||
|
||
Parameters
|
||
----------
|
||
T : str
|
||
Label of tensor dataset.
|
||
|
||
"""
|
||
def _add_deviator(T):
|
||
|
||
if not np.all(np.array(T['data'].shape[1:]) == np.array([3,3])):
|
||
raise ValueError
|
||
|
||
return {
|
||
'data': mechanics.deviatoric_part(T['data']),
|
||
'label': 's_{}'.format(T['label']),
|
||
'meta': {
|
||
'Unit': T['meta']['Unit'],
|
||
'Description': 'Deviator of tensor {} ({})'.format(T['label'],T['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_deviator v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_deviator,{'T':T})
|
||
|
||
|
||
def add_eigenvalues(self,S):
|
||
"""
|
||
Add eigenvalues of symmetric tensor.
|
||
|
||
Parameters
|
||
----------
|
||
S : str
|
||
Label of symmetric tensor dataset.
|
||
|
||
"""
|
||
def _add_eigenvalue(S):
|
||
|
||
return {
|
||
'data': mechanics.eigenvalues(S['data']),
|
||
'label': 'lambda({})'.format(S['label']),
|
||
'meta' : {
|
||
'Unit': S['meta']['Unit'],
|
||
'Description': 'Eigenvalues of {} ({})'.format(S['label'],S['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_eigenvalues v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_eigenvalue,{'S':S})
|
||
|
||
|
||
def add_eigenvectors(self,S):
|
||
"""
|
||
Add eigenvectors of symmetric tensor.
|
||
|
||
Parameters
|
||
----------
|
||
S : str
|
||
Label of symmetric tensor dataset.
|
||
|
||
"""
|
||
def _add_eigenvector(S):
|
||
|
||
return {
|
||
'data': mechanics.eigenvectors(S['data']),
|
||
'label': 'v({})'.format(S['label']),
|
||
'meta' : {
|
||
'Unit': '1',
|
||
'Description': 'Eigenvectors of {} ({})'.format(S['label'],S['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_eigenvectors v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_eigenvector,{'S':S})
|
||
|
||
|
||
def add_IPFcolor(self,q,l):
|
||
"""
|
||
Add RGB color tuple of inverse pole figure (IPF) color.
|
||
|
||
Parameters
|
||
----------
|
||
q : str
|
||
Label of the dataset containing the crystallographic orientation as quaternions.
|
||
l : numpy.array of shape (3)
|
||
Lab frame direction for inverse pole figure.
|
||
|
||
"""
|
||
def _add_IPFcolor(q,l):
|
||
|
||
d = np.array(l)
|
||
d_unit = d/np.linalg.norm(d)
|
||
m = util.scale_to_coprime(d)
|
||
colors = np.empty((len(q['data']),3),np.uint8)
|
||
|
||
lattice = q['meta']['Lattice']
|
||
|
||
for i,q in enumerate(q['data']):
|
||
o = Orientation(np.array([q['w'],q['x'],q['y'],q['z']]),lattice).reduced()
|
||
colors[i] = np.uint8(o.IPFcolor(d_unit)*255)
|
||
|
||
return {
|
||
'data': colors,
|
||
'label': 'IPFcolor_[{} {} {}]'.format(*m),
|
||
'meta' : {
|
||
'Unit': 'RGB (8bit)',
|
||
'Lattice': lattice,
|
||
'Description': 'Inverse Pole Figure (IPF) colors for direction/plane [{} {} {})'.format(*m),
|
||
'Creator': 'dadf5.py:add_IPFcolor v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_IPFcolor,{'q':q},{'l':l})
|
||
|
||
|
||
def add_maximum_shear(self,S):
|
||
"""
|
||
Add maximum shear components of symmetric tensor.
|
||
|
||
Parameters
|
||
----------
|
||
S : str
|
||
Label of symmetric tensor dataset.
|
||
|
||
"""
|
||
def _add_maximum_shear(S):
|
||
|
||
return {
|
||
'data': mechanics.maximum_shear(S['data']),
|
||
'label': 'max_shear({})'.format(S['label']),
|
||
'meta': {
|
||
'Unit': S['meta']['Unit'],
|
||
'Description': 'Maximum shear component of {} ({})'.format(S['label'],S['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_maximum_shear v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_maximum_shear,{'S':S})
|
||
|
||
|
||
def add_Mises(self,S):
|
||
"""
|
||
Add the equivalent Mises stress or strain of a symmetric tensor.
|
||
|
||
Parameters
|
||
----------
|
||
S : str
|
||
Label of symmetric tensorial stress or strain dataset.
|
||
|
||
"""
|
||
def _add_Mises(S):
|
||
|
||
t = 'strain' if S['meta']['Unit'] == '1' else \
|
||
'stress'
|
||
return {
|
||
'data': mechanics.Mises_strain(S['data']) if t=='strain' else mechanics.Mises_stress(S['data']),
|
||
'label': '{}_vM'.format(S['label']),
|
||
'meta': {
|
||
'Unit': S['meta']['Unit'],
|
||
'Description': 'Mises equivalent {} of {} ({})'.format(t,S['label'],S['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_Mises v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_Mises,{'S':S})
|
||
|
||
|
||
def add_norm(self,x,ord=None):
|
||
"""
|
||
Add the norm of vector or tensor.
|
||
|
||
Parameters
|
||
----------
|
||
x : str
|
||
Label of vector or tensor dataset.
|
||
ord : {non-zero int, inf, -inf, ‘fro’, ‘nuc’}, optional
|
||
Order of the norm. inf means NumPy’s inf object. For details refer to numpy.linalg.norm.
|
||
|
||
"""
|
||
def _add_norm(x,ord):
|
||
|
||
o = ord
|
||
if len(x['data'].shape) == 2:
|
||
axis = 1
|
||
t = 'vector'
|
||
if o is None: o = 2
|
||
elif len(x['data'].shape) == 3:
|
||
axis = (1,2)
|
||
t = 'tensor'
|
||
if o is None: o = 'fro'
|
||
else:
|
||
raise ValueError
|
||
|
||
return {
|
||
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
|
||
'label': '|{}|_{}'.format(x['label'],o),
|
||
'meta': {
|
||
'Unit': x['meta']['Unit'],
|
||
'Description': '{}-norm of {} {} ({})'.format(ord,t,x['label'],x['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_norm v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_norm,{'x':x},{'ord':ord})
|
||
|
||
|
||
def add_PK2(self,P='P',F='F'):
|
||
"""
|
||
Add 2. Piola-Kirchhoff calculated from first Piola-Kirchhoff stress and deformation gradient.
|
||
|
||
Parameters
|
||
----------
|
||
P : str, optional
|
||
Label first Piola-Kirchhoff stress dataset. Defaults to ‘P’.
|
||
F : str, optional
|
||
Label of deformation gradient dataset. Defaults to ‘F’.
|
||
|
||
"""
|
||
def _add_PK2(P,F):
|
||
|
||
return {
|
||
'data': mechanics.PK2(P['data'],F['data']),
|
||
'label': 'S',
|
||
'meta': {
|
||
'Unit': P['meta']['Unit'],
|
||
'Description': '2. Kirchhoff stress calculated from {} ({}) '.format(P['label'],
|
||
P['meta']['Description'])+\
|
||
'and {} ({})'.format(F['label'],F['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_PK2 v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_PK2,{'P':P,'F':F})
|
||
|
||
|
||
def add_pole(self,q,p,polar=False):
|
||
"""
|
||
Add coordinates of stereographic projection of given pole in crystal frame.
|
||
|
||
Parameters
|
||
----------
|
||
q : str
|
||
Label of the dataset containing the crystallographic orientation as quaternions.
|
||
p : numpy.array of shape (3)
|
||
Crystallographic direction or plane.
|
||
polar : bool, optional
|
||
Give pole in polar coordinates. Defaults to False.
|
||
|
||
"""
|
||
def _add_pole(q,p,polar):
|
||
|
||
pole = np.array(p)
|
||
unit_pole = pole/np.linalg.norm(pole)
|
||
m = util.scale_to_coprime(pole)
|
||
coords = np.empty((len(q['data']),2))
|
||
|
||
for i,q in enumerate(q['data']):
|
||
o = Rotation(np.array([q['w'],q['x'],q['y'],q['z']]))
|
||
rotatedPole = o*unit_pole # rotate pole according to crystal orientation
|
||
(x,y) = rotatedPole[0:2]/(1.+abs(unit_pole[2])) # stereographic projection
|
||
coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y]
|
||
|
||
return {
|
||
'data': coords,
|
||
'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
|
||
'meta' : {
|
||
'Unit': '1',
|
||
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
|
||
.format('Polar' if polar else 'Cartesian'),
|
||
'Creator' : 'dadf5.py:add_pole v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_pole,{'q':q},{'p':p,'polar':polar})
|
||
|
||
|
||
def add_rotational_part(self,F):
|
||
"""
|
||
Add rotational part of a deformation gradient.
|
||
|
||
Parameters
|
||
----------
|
||
F : str, optional
|
||
Label of deformation gradient dataset.
|
||
|
||
"""
|
||
def _add_rotational_part(F):
|
||
|
||
return {
|
||
'data': mechanics.rotational_part(F['data']),
|
||
'label': 'R({})'.format(F['label']),
|
||
'meta': {
|
||
'Unit': F['meta']['Unit'],
|
||
'Description': 'Rotational part of {} ({})'.format(F['label'],F['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_rotational_part v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_rotational_part,{'F':F})
|
||
|
||
|
||
def add_spherical(self,T):
|
||
"""
|
||
Add the spherical (hydrostatic) part of a tensor.
|
||
|
||
Parameters
|
||
----------
|
||
T : str
|
||
Label of tensor dataset.
|
||
|
||
"""
|
||
def _add_spherical(T):
|
||
|
||
if not np.all(np.array(T['data'].shape[1:]) == np.array([3,3])):
|
||
raise ValueError
|
||
|
||
return {
|
||
'data': mechanics.spherical_part(T['data']),
|
||
'label': 'p_{}'.format(T['label']),
|
||
'meta': {
|
||
'Unit': T['meta']['Unit'],
|
||
'Description': 'Spherical component of tensor {} ({})'.format(T['label'],T['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_spherical v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_spherical,{'T':T})
|
||
|
||
|
||
def add_strain_tensor(self,F='F',t='V',m=0.0):
|
||
"""
|
||
Add strain tensor of a deformation gradient.
|
||
|
||
For details refer to damask.mechanics.strain_tensor
|
||
|
||
Parameters
|
||
----------
|
||
F : str, optional
|
||
Label of deformation gradient dataset. Defaults to ‘F’.
|
||
t : {‘V’, ‘U’}, optional
|
||
Type of the polar decomposition, ‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
|
||
Defaults to ‘V’.
|
||
m : float, optional
|
||
Order of the strain calculation. Defaults to ‘0.0’.
|
||
|
||
"""
|
||
def _add_strain_tensor(F,t,m):
|
||
|
||
return {
|
||
'data': mechanics.strain_tensor(F['data'],t,m),
|
||
'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
|
||
'meta': {
|
||
'Unit': F['meta']['Unit'],
|
||
'Description': 'Strain tensor of {} ({})'.format(F['label'],F['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_strain_tensor v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_strain_tensor,{'F':F},{'t':t,'m':m})
|
||
|
||
|
||
def add_stretch_tensor(self,F='F',t='V'):
|
||
"""
|
||
Add stretch tensor of a deformation gradient.
|
||
|
||
Parameters
|
||
----------
|
||
F : str, optional
|
||
Label of deformation gradient dataset. Defaults to ‘F’.
|
||
t : {‘V’, ‘U’}, optional
|
||
Type of the polar decomposition, ‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
|
||
Defaults to ‘V’.
|
||
|
||
"""
|
||
def _add_stretch_tensor(F,t):
|
||
|
||
return {
|
||
'data': mechanics.left_stretch(F['data']) if t == 'V' else mechanics.right_stretch(F['data']),
|
||
'label': '{}({})'.format(t,F['label']),
|
||
'meta': {
|
||
'Unit': F['meta']['Unit'],
|
||
'Description': '{} stretch tensor of {} ({})'.format('Left' if t == 'V' else 'Right',
|
||
F['label'],F['meta']['Description']),
|
||
'Creator': 'dadf5.py:add_stretch_tensor v{}'.format(version)
|
||
}
|
||
}
|
||
|
||
self.__add_generic_pointwise(_add_stretch_tensor,{'F':F},{'t':t})
|
||
|
||
|
||
def __add_generic_pointwise(self,func,dataset_mapping,args={}):
|
||
"""
|
||
General function to add pointwise data.
|
||
|
||
Parameters
|
||
----------
|
||
func : function
|
||
Function that calculates a new dataset from one or more datasets per HDF5 group.
|
||
dataset_mapping : dictionary
|
||
Mapping HDF5 data label to callback function argument
|
||
extra_args : dictionary, optional
|
||
Any extra arguments parsed to func.
|
||
|
||
"""
|
||
def job(args):
|
||
"""Call function with input data + extra arguments, returns results + group."""
|
||
args['results'].put({**args['func'](**args['in']),'group':args['group']})
|
||
|
||
env = Environment()
|
||
N_threads = int(env.options['DAMASK_NUM_THREADS'])
|
||
N_threads //=N_threads # disable for the moment
|
||
|
||
results = Queue(N_threads)
|
||
pool = util.ThreadPool(N_threads)
|
||
N_added = N_threads + 1
|
||
|
||
todo = []
|
||
# ToDo: It would be more memory efficient to read only from file when required, i.e. do to it in pool.add_task
|
||
for group in self.groups_with_datasets(dataset_mapping.values()):
|
||
with h5py.File(self.fname,'r') as f:
|
||
datasets_in = {}
|
||
for arg,label in dataset_mapping.items():
|
||
loc = f[group+'/'+label]
|
||
data = loc[()]
|
||
meta = {k:loc.attrs[k].decode() for k in loc.attrs.keys()}
|
||
datasets_in[arg] = {'data': data, 'meta': meta, 'label': label}
|
||
|
||
todo.append({'in':{**datasets_in,**args},'func':func,'group':group,'results':results})
|
||
|
||
pool.map(job, todo[:N_added]) # initialize
|
||
|
||
N_not_calculated = len(todo)
|
||
while N_not_calculated > 0:
|
||
result = results.get()
|
||
with h5py.File(self.fname,'a') as f: # write to file
|
||
dataset_out = f[result['group']].create_dataset(result['label'],data=result['data'])
|
||
for k in result['meta'].keys():
|
||
dataset_out.attrs[k] = result['meta'][k].encode()
|
||
N_not_calculated-=1
|
||
|
||
if N_added < len(todo): # add more jobs
|
||
pool.add_task(job,todo[N_added])
|
||
N_added +=1
|
||
|
||
pool.wait_completion()
|
||
|
||
|
||
def to_vtk(self,labels,mode='cell'):
|
||
"""
|
||
Export to vtk cell/point data.
|
||
|
||
Parameters
|
||
----------
|
||
labels : str or list of
|
||
Labels of the datasets to be exported.
|
||
mode : str, either 'cell' or 'point'
|
||
Export in cell format or point format.
|
||
Defaults to 'cell'.
|
||
|
||
"""
|
||
if mode.lower()=='cell':
|
||
|
||
if self.structured:
|
||
|
||
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
|
||
for dim in [0,1,2]:
|
||
for c in np.linspace(0,self.size[dim],1+self.grid[dim]):
|
||
coordArray[dim].InsertNextValue(c)
|
||
|
||
vtk_geom = vtk.vtkRectilinearGrid()
|
||
vtk_geom.SetDimensions(*(self.grid+1))
|
||
vtk_geom.SetXCoordinates(coordArray[0])
|
||
vtk_geom.SetYCoordinates(coordArray[1])
|
||
vtk_geom.SetZCoordinates(coordArray[2])
|
||
|
||
else:
|
||
|
||
nodes = vtk.vtkPoints()
|
||
with h5py.File(self.fname,'r') as f:
|
||
nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
|
||
|
||
vtk_geom = vtk.vtkUnstructuredGrid()
|
||
vtk_geom.SetPoints(nodes)
|
||
vtk_geom.Allocate(f['/geometry/T_c'].shape[0])
|
||
|
||
if self.version_major == 0 and self.version_minor <= 5:
|
||
vtk_type = vtk.VTK_HEXAHEDRON
|
||
n_nodes = 8
|
||
else:
|
||
if f['/geometry/T_c'].attrs['VTK_TYPE'] == b'TRIANGLE':
|
||
vtk_type = vtk.VTK_TRIANGLE
|
||
n_nodes = 3
|
||
elif f['/geometry/T_c'].attrs['VTK_TYPE'] == b'QUAD':
|
||
vtk_type = vtk.VTK_QUAD
|
||
n_nodes = 4
|
||
elif f['/geometry/T_c'].attrs['VTK_TYPE'] == b'TETRA': # not tested
|
||
vtk_type = vtk.VTK_TETRA
|
||
n_nodes = 4
|
||
elif f['/geometry/T_c'].attrs['VTK_TYPE'] == b'HEXAHEDRON':
|
||
vtk_type = vtk.VTK_HEXAHEDRON
|
||
n_nodes = 8
|
||
|
||
for i in f['/geometry/T_c']:
|
||
vtk_geom.InsertNextCell(vtk_type,n_nodes,i-1)
|
||
|
||
elif mode.lower()=='point':
|
||
Points = vtk.vtkPoints()
|
||
Vertices = vtk.vtkCellArray()
|
||
for c in self.cell_coordinates():
|
||
pointID = Points.InsertNextPoint(c)
|
||
Vertices.InsertNextCell(1)
|
||
Vertices.InsertCellPoint(pointID)
|
||
|
||
vtk_geom = vtk.vtkPolyData()
|
||
vtk_geom.SetPoints(Points)
|
||
vtk_geom.SetVerts(Vertices)
|
||
vtk_geom.Modified()
|
||
|
||
N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
|
||
|
||
for i,inc in enumerate(self.iter_visible('increments')):
|
||
vtk_data = []
|
||
|
||
materialpoints_backup = self.selection['materialpoints'].copy()
|
||
self.set_visible('materialpoints',False)
|
||
for label in (labels if isinstance(labels,list) else [labels]):
|
||
for p in self.iter_visible('con_physics'):
|
||
if p != 'generic':
|
||
for c in self.iter_visible('constituents'):
|
||
x = self.get_dataset_location(label)
|
||
if len(x) == 0:
|
||
continue
|
||
array = self.read_dataset(x,0)
|
||
shape = [array.shape[0],np.product(array.shape[1:])]
|
||
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
|
||
deep=True,array_type= vtk.VTK_DOUBLE))
|
||
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
|
||
vtk_geom.GetCellData().AddArray(vtk_data[-1])
|
||
|
||
else:
|
||
x = self.get_dataset_location(label)
|
||
if len(x) == 0:
|
||
continue
|
||
array = self.read_dataset(x,0)
|
||
shape = [array.shape[0],np.product(array.shape[1:])]
|
||
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
|
||
deep=True,array_type= vtk.VTK_DOUBLE))
|
||
ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name
|
||
dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name
|
||
vtk_data[-1].SetName(dset_name)
|
||
vtk_geom.GetCellData().AddArray(vtk_data[-1])
|
||
|
||
self.set_visible('materialpoints',materialpoints_backup)
|
||
|
||
constituents_backup = self.selection['constituents'].copy()
|
||
self.set_visible('constituents',False)
|
||
for label in (labels if isinstance(labels,list) else [labels]):
|
||
for p in self.iter_visible('mat_physics'):
|
||
if p != 'generic':
|
||
for m in self.iter_visible('materialpoints'):
|
||
x = self.get_dataset_location(label)
|
||
if len(x) == 0:
|
||
continue
|
||
array = self.read_dataset(x,0)
|
||
shape = [array.shape[0],np.product(array.shape[1:])]
|
||
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
|
||
deep=True,array_type= vtk.VTK_DOUBLE))
|
||
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
|
||
vtk_geom.GetCellData().AddArray(vtk_data[-1])
|
||
else:
|
||
x = self.get_dataset_location(label)
|
||
if len(x) == 0:
|
||
continue
|
||
array = self.read_dataset(x,0)
|
||
shape = [array.shape[0],np.product(array.shape[1:])]
|
||
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
|
||
deep=True,array_type= vtk.VTK_DOUBLE))
|
||
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
|
||
vtk_geom.GetCellData().AddArray(vtk_data[-1])
|
||
self.set_visible('constituents',constituents_backup)
|
||
|
||
if mode.lower()=='cell':
|
||
writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
|
||
vtk.vtkXMLUnstructuredGridWriter()
|
||
x = self.get_dataset_location('u_n')
|
||
vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0),
|
||
deep=True,array_type=vtk.VTK_DOUBLE))
|
||
vtk_data[-1].SetName('u')
|
||
vtk_geom.GetPointData().AddArray(vtk_data[-1])
|
||
elif mode.lower()=='point':
|
||
writer = vtk.vtkXMLPolyDataWriter()
|
||
|
||
|
||
file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
|
||
inc[3:].zfill(N_digits),
|
||
writer.GetDefaultFileExtension())
|
||
|
||
writer.SetCompressorTypeToZLib()
|
||
writer.SetDataModeToBinary()
|
||
writer.SetFileName(file_out)
|
||
writer.SetInputData(vtk_geom)
|
||
|
||
writer.Write()
|