Merge branch 'properly-close-files' into 'development'

use context manager to ensure that opened files are closed

See merge request damask/DAMASK!884
This commit is contained in:
Philip Eisenlohr 2023-12-23 17:49:54 +00:00
commit b22251a2b9
5 changed files with 69 additions and 79 deletions

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@ -2,7 +2,7 @@ import os
import json import json
import functools import functools
import colorsys import colorsys
from typing import Optional, Union, TextIO from typing import Optional, Union
from itertools import chain from itertools import chain
import numpy as np import numpy as np
@ -344,30 +344,6 @@ class Colormap(mpl.colors.ListedColormap):
return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name) return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
def _get_file_handle(self,
fname: Union[FileHandle, None],
suffix: str = '') -> TextIO:
"""
Provide file handle.
Parameters
----------
fname : file, str, pathlib.Path, or None
Name or handle of file.
If None, colormap name + suffix.
suffix: str, optional
Extension to use for colormap file.
Defaults to empty.
Returns
-------
f : file object
File handle with write access.
"""
return util.open_text(self.name.replace(' ','_')+suffix if fname is None else fname, 'w')
def save_paraview(self, def save_paraview(self,
fname: Optional[FileHandle] = None): fname: Optional[FileHandle] = None):
""" """
@ -387,9 +363,9 @@ class Colormap(mpl.colors.ListedColormap):
'RGBPoints':list(chain.from_iterable([(i,*c) for i,c in enumerate(self.colors.round(6))])) 'RGBPoints':list(chain.from_iterable([(i,*c) for i,c in enumerate(self.colors.round(6))]))
}] }]
fhandle = self._get_file_handle(fname,'.json') with util.open_text(self.name.replace(' ','_')+'.json' if fname is None else fname, 'w') as fhandle:
json.dump(out,fhandle,indent=4) json.dump(out,fhandle,indent=4)
fhandle.write('\n') fhandle.write('\n')
def save_ASCII(self, def save_ASCII(self,
@ -405,7 +381,9 @@ class Colormap(mpl.colors.ListedColormap):
""" """
labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3} labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}']) t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}'])
t.save(self._get_file_handle(fname,'.txt'))
with util.open_text(self.name.replace(' ','_')+'.txt' if fname is None else fname, 'w') as fhandle:
t.save(fhandle)
def save_GOM(self, fname: Optional[FileHandle] = None): def save_GOM(self, fname: Optional[FileHandle] = None):
@ -425,7 +403,8 @@ class Colormap(mpl.colors.ListedColormap):
+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(np.int64))]) \ + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(np.int64))]) \
+ '\n' + '\n'
self._get_file_handle(fname,'.legend').write(GOM_str) with util.open_text(self.name.replace(' ','_')+'.legend' if fname is None else fname, 'w') as fhandle:
fhandle.write(GOM_str)
def save_gmsh(self, def save_gmsh(self,
@ -443,7 +422,9 @@ class Colormap(mpl.colors.ListedColormap):
gmsh_str = 'View.ColorTable = {\n' \ gmsh_str = 'View.ColorTable = {\n' \
+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \ +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
+'\n}\n' +'\n}\n'
self._get_file_handle(fname,'.msh').write(gmsh_str)
with util.open_text(self.name.replace(' ','_')+'.msh' if fname is None else fname, 'w') as fhandle:
fhandle.write(gmsh_str)
@staticmethod @staticmethod

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@ -70,9 +70,9 @@ class LoadcaseGrid(YAML):
if key not in kwargs: if key not in kwargs:
kwargs[key] = default kwargs[key] = default
fhandle = util.open_text(fname,'w') with util.open_text(fname,'w') as fhandle:
try: try:
fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs)) fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
except TypeError: # compatibility with old pyyaml except TypeError: # compatibility with old pyyaml
del kwargs['sort_keys'] del kwargs['sort_keys']
fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs)) fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))

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@ -277,28 +277,28 @@ class Table:
Table data from file. Table data from file.
""" """
f = util.open_text(fname) with util.open_text(fname) as f:
f.seek(0) f.seek(0)
comments = [] comments = []
while (line := f.readline().strip()).startswith('#'): while (line := f.readline().strip()).startswith('#'):
comments.append(line.lstrip('#').strip()) comments.append(line.lstrip('#').strip())
labels = line.split() labels = line.split()
shapes = {} shapes = {}
for label in labels: for label in labels:
tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label) tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
if tensor_column: if tensor_column:
my_shape = tensor_column.group().split(':',1)[0].split('x') my_shape = tensor_column.group().split(':',1)[0].split('x')
shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape]) shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
else:
vector_column = re.match(r'[0-9]*?_',label)
if vector_column:
shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
else: else:
shapes[label] = (1,) vector_column = re.match(r'[0-9]*?_',label)
if vector_column:
shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
else:
shapes[label] = (1,)
data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+') data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
return Table(shapes,data,comments) return Table(shapes,data,comments)
@ -339,10 +339,9 @@ class Table:
Table data from file. Table data from file.
""" """
f = util.open_text(fname) with util.open_text(fname) as f:
f.seek(0) f.seek(0)
content = f.readlines()
content = f.readlines()
comments = [util.execution_stamp('Table','from_ang')] comments = [util.execution_stamp('Table','from_ang')]
for line in content: for line in content:
@ -605,10 +604,9 @@ class Table:
labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \ labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
for i in range(np.prod(self.shapes[l]))] for i in range(np.prod(self.shapes[l]))]
f = util.open_text(fname,'w') with util.open_text(fname,'w') as f:
f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else '')) try: # backward compatibility
try: # backward compatibility self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n')
self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n') except TypeError:
except TypeError: self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')
self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')

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@ -197,7 +197,9 @@ class YAML(dict):
YAML from file. YAML from file.
""" """
return cls(yaml.load(util.open_text(fname), Loader=SafeLoader)) with util.open_text(fname) as fhandle:
return cls(yaml.load(fhandle, Loader=SafeLoader))
def save(self, def save(self,
fname: FileHandle, fname: FileHandle,
@ -220,12 +222,12 @@ class YAML(dict):
if 'sort_keys' not in kwargs: if 'sort_keys' not in kwargs:
kwargs['sort_keys'] = False kwargs['sort_keys'] = False
fhandle = util.open_text(fname,'w') with util.open_text(fname,'w') as fhandle:
try: try:
fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs)) fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
except TypeError: # compatibility with old pyyaml except TypeError: # compatibility with old pyyaml
del kwargs['sort_keys'] del kwargs['sort_keys']
fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs)) fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
@property @property

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@ -8,12 +8,13 @@ import shlex as _shlex
import re as _re import re as _re
import signal as _signal import signal as _signal
import fractions as _fractions import fractions as _fractions
import contextlib as _contextlib
from collections import abc as _abc, OrderedDict as _OrderedDict from collections import abc as _abc, OrderedDict as _OrderedDict
from functools import reduce as _reduce, partial as _partial, wraps as _wraps from functools import reduce as _reduce, partial as _partial, wraps as _wraps
import inspect import inspect
from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \ from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \ Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
Any as _Any, TextIO as _TextIO Any as _Any, TextIO as _TextIO, Generator as _Generator
from pathlib import Path as _Path from pathlib import Path as _Path
import numpy as _np import numpy as _np
@ -193,11 +194,15 @@ def run(cmd: str,
return stdout, stderr return stdout, stderr
@_contextlib.contextmanager
def open_text(fname: _FileHandle, def open_text(fname: _FileHandle,
mode: _Literal['r','w'] = 'r') -> _TextIO: # noqa mode: _Literal['r','w'] = 'r') -> _Generator[_TextIO, None, None]: # noqa
""" """
Open a text file. Open a text file with Unix line endings
If a path or string is given, a context manager ensures that
the file handle is closed.
If a file handle is given, it remains unmodified.
Parameters Parameters
---------- ----------
@ -211,8 +216,12 @@ def open_text(fname: _FileHandle,
f : file handle f : file handle
""" """
return fname if not isinstance(fname, (str,_Path)) else \ if isinstance(fname, (str,_Path)):
open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None)) fhandle = open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
yield fhandle
fhandle.close()
else:
yield fname
def execution_stamp(class_name: str, def execution_stamp(class_name: str,