modified file writing of geom and table to a general to_file() that takes a "format=" argument
This commit is contained in:
Philip Eisenlohr
parent
2f1e064435
commit
a4785ba562
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@ -300,9 +300,9 @@ class Colormap(mpl.colors.ListedColormap):
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if fhandle is None:
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with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:
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t.to_ASCII(f,True)
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t.to_file(f,new_style=True)
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else:
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t.to_ASCII(fhandle,True)
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t.to_file(fhandle,new_style=True)
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@staticmethod
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def _export_GOM(colormap,fhandle=None):
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@ -447,7 +447,7 @@ class Geom:
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)
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def to_file(self,fname,pack=None):
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def to_file(self,fname,format='vtr',pack=None):
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"""
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Writes a geom file.
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@ -455,94 +455,120 @@ class Geom:
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----------
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fname : str or file handle
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Geometry file to write.
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format : {'vtr', 'ASCII'}, optional
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File format, defaults to 'vtr'. Available formats are:
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- vtr: VTK rectilinear grid file, extension '.vtr'.
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- ASCII: Plain text file, extension '.geom'.
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pack : bool, optional
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Compress geometry with 'x of y' and 'a to b'.
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Compress ASCII geometry with 'x of y' and 'a to b'.
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"""
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header = [f'{len(self.comments)+4} header'] + self.comments
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header.append('grid a {} b {} c {}'.format(*self.get_grid()))
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header.append('size x {} y {} z {}'.format(*self.get_size()))
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header.append('origin x {} y {} z {}'.format(*self.get_origin()))
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header.append(f'homogenization {self.get_homogenization()}')
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def _to_ASCII(geom,fname,pack=None):
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"""
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Writes a geom file.
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grid = self.get_grid()
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Parameters
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----------
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geom : Geom object
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Geometry to write.
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fname : str or file handle
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Geometry file to write.
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pack : bool, optional
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Compress geometry with 'x of y' and 'a to b'.
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if pack is None:
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plain = grid.prod()/self.N_microstructure < 250
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"""
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header = [f'{len(geom.comments)+4} header'] + geom.comments
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header.append('grid a {} b {} c {}'.format(*geom.get_grid()))
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header.append('size x {} y {} z {}'.format(*geom.get_size()))
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header.append('origin x {} y {} z {}'.format(*geom.get_origin()))
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header.append(f'homogenization {geom.get_homogenization()}')
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grid = geom.get_grid()
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if pack is None:
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plain = grid.prod()/geom.N_microstructure < 250
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else:
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plain = not pack
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if plain:
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format_string = '%g' if geom.microstructure.dtype in np.sctypes['float'] else \
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'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(geom.microstructure)))))
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np.savetxt(fname,
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geom.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
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header='\n'.join(header), fmt=format_string, comments='')
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else:
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try:
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f = open(fname,'w')
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except TypeError:
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f = fname
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compressType = None
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former = start = -1
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reps = 0
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for current in geom.microstructure.flatten('F'):
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if abs(current - former) == 1 and (start - current) == reps*(former - current):
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compressType = 'to'
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reps += 1
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elif current == former and start == former:
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compressType = 'of'
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reps += 1
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else:
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if compressType is None:
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f.write('\n'.join(header)+'\n')
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elif compressType == '.':
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f.write(f'{former}\n')
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elif compressType == 'to':
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f.write(f'{start} to {former}\n')
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elif compressType == 'of':
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f.write(f'{reps} of {former}\n')
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compressType = '.'
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start = current
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reps = 1
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former = current
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if compressType == '.':
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f.write(f'{former}\n')
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elif compressType == 'to':
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f.write(f'{start} to {former}\n')
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elif compressType == 'of':
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f.write(f'{reps} of {former}\n')
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def _to_vtr(geom,fname=None):
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"""
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Generates vtk rectilinear grid.
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Parameters
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----------
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geom : Geom object
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Geometry to write.
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fname : str, optional
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Filename to write. If no file is given, a string is returned.
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Valid extension is .vtr, it will be appended if not given.
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"""
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v = VTK.from_rectilinearGrid(geom.grid,geom.size,geom.origin)
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v.add(geom.microstructure.flatten(order='F'),'materialpoint')
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v.add_comments(geom.comments)
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if fname:
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v.to_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
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else:
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sys.stdout.write(v.__repr__())
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if format.lower() == 'ascii':
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return _to_ASCII(self,fname,pack)
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elif format.lower() == 'vtr':
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return _to_vtr(self,fname)
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else:
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plain = not pack
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raise TypeError(f'Unknown format {format}.')
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if plain:
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format_string = '%g' if self.microstructure.dtype in np.sctypes['float'] else \
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'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
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np.savetxt(fname,
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self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
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header='\n'.join(header), fmt=format_string, comments='')
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else:
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try:
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f = open(fname,'w')
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except TypeError:
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f = fname
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compressType = None
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former = start = -1
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reps = 0
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for current in self.microstructure.flatten('F'):
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if abs(current - former) == 1 and (start - current) == reps*(former - current):
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compressType = 'to'
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reps += 1
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elif current == former and start == former:
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compressType = 'of'
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reps += 1
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else:
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if compressType is None:
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f.write('\n'.join(header)+'\n')
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elif compressType == '.':
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f.write(f'{former}\n')
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elif compressType == 'to':
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f.write(f'{start} to {former}\n')
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elif compressType == 'of':
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f.write(f'{reps} of {former}\n')
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compressType = '.'
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start = current
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reps = 1
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former = current
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if compressType == '.':
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f.write(f'{former}\n')
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elif compressType == 'to':
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f.write(f'{start} to {former}\n')
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elif compressType == 'of':
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f.write(f'{reps} of {former}\n')
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def to_vtr(self,fname=None):
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"""
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Generates vtk rectilinear grid.
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Parameters
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----------
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fname : str, optional
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Filename to write. If no file is given, a string is returned.
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Valid extension is .vtr, it will be appended if not given.
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"""
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v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
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v.add(self.microstructure.flatten(order='F'),'materialpoint')
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v.add_comments(self.comments)
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if fname:
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v.to_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
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else:
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sys.stdout.write(v.__repr__())
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def as_ASCII(self):
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def as_ASCII(self,pack=False):
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"""Format geometry as human-readable ASCII."""
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f = StringIO()
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self.to_file(f)
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self.to_file(f,'ASCII',pack)
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f.seek(0)
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return ''.join(f.readlines())
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@ -313,7 +313,7 @@ class Table:
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self.shapes[key] = other.shapes[key]
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def to_ASCII(self,fname,new_style=False):
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def to_file(self,fname,format='ASCII',new_style=False):
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"""
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Store as plain text file.
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@ -321,32 +321,51 @@ class Table:
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----------
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fname : file, str, or pathlib.Path
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Filename or file for writing.
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format : {ASCII'}, optional
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File format, defaults to 'ASCII'. Available formats are:
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- ASCII: Plain text file, extension '.txt'.
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new_style : Boolean, optional
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Write table in new style, indicating header lines by comment sign ('#') only.
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"""
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seen = set()
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labels = []
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for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
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if self.shapes[l] == (1,):
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labels.append(f'{l}')
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elif len(self.shapes[l]) == 1:
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labels += [f'{i+1}_{l}' \
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for i in range(self.shapes[l][0])]
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else:
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labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(self.shapes[l]))]
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def _to_ASCII(table,fname,new_style=False):
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"""
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Store as plain text file.
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if new_style:
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header = [f'# {comment}' for comment in self.comments]
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Parameters
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----------
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table : Table object
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Table to write.
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fname : file, str, or pathlib.Path
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Filename or file for writing.
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new_style : Boolean, optional
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Write table in new style, indicating header lines by comment sign ('#') only.
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"""
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seen = set()
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labels = []
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for l in [x for x in table.data.columns if not (x in seen or seen.add(x))]:
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if table.shapes[l] == (1,):
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labels.append(f'{l}')
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elif len(table.shapes[l]) == 1:
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labels += [f'{i+1}_{l}' \
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for i in range(table.shapes[l][0])]
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else:
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labels += [f'{util.srepr(table.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(table.shapes[l]))]
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header = [f'# {comment}' for comment in table.comments] if new_style else \
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[f'{len(table.comments)+1} header'] + table.comments
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try:
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f = open(fname,'w')
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except TypeError:
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f = fname
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for line in header + [' '.join(labels)]: f.write(line+'\n')
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table.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
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if format.lower() == 'ascii':
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return _to_ASCII(self,fname,new_style)
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else:
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header = [f'{len(self.comments)+1} header'] \
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+ self.comments \
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try:
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f = open(fname,'w')
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except TypeError:
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f = fname
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for line in header + [' '.join(labels)]: f.write(line+'\n')
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self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
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raise TypeError(f'Unknown format {format}.')
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@ -63,13 +63,13 @@ class TestGeom:
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def test_write_read_str(self,default,tmpdir):
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default.to_file(str(tmpdir/'default.geom'))
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default.to_file(str(tmpdir/'default.geom'),format='ASCII')
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new = Geom.from_file(str(tmpdir/'default.geom'))
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assert geom_equal(default,new)
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def test_write_read_file(self,default,tmpdir):
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with open(tmpdir/'default.geom','w') as f:
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default.to_file(f,pack=True)
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default.to_file(f,format='ASCII',pack=True)
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with open(tmpdir/'default.geom') as f:
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new = Geom.from_file(f)
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assert geom_equal(default,new)
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@ -82,8 +82,7 @@ class TestGeom:
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assert geom_equal(default,new)
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def test_read_write_vtr(self,default,tmpdir):
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default.to_vtr(tmpdir/'default')
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print(default.to_vtr())
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default.to_file(tmpdir/'default',format='vtr')
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for _ in range(10):
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time.sleep(.2)
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if os.path.exists(tmpdir/'default.vtr'): break
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@ -110,7 +109,7 @@ class TestGeom:
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@pytest.mark.parametrize('pack',[True,False])
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def test_pack(self,default,tmpdir,pack):
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default.to_file(tmpdir/'default.geom',pack=pack)
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default.to_file(tmpdir/'default.geom',format='ASCII',pack=pack)
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new = Geom.from_file(tmpdir/'default.geom')
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assert geom_equal(new,default)
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@ -140,6 +139,10 @@ class TestGeom:
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with pytest.raises(TypeError):
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default.set_homogenization(homogenization=0)
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def test_invalid_write_format(self,default):
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with pytest.raises(TypeError):
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default.to_file(format='invalid')
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@pytest.mark.parametrize('directions,reflect',[
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(['x'], False),
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(['x','y','z'],True),
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@ -196,7 +199,7 @@ class TestGeom:
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current = default.clean(stencil,selection,periodic)
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reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
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if update and stencil > 1:
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current.to_vtr(reference)
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current.to_file(reference,format='vtr')
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for _ in range(10):
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time.sleep(.2)
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if os.path.exists(reference.with_suffix('.vtr')): break
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@ -35,7 +35,7 @@ class TestTable:
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@pytest.mark.parametrize('mode',['str','path'])
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def test_write_read(self,default,tmpdir,mode):
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default.to_ASCII(tmpdir/'default.txt')
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default.to_file(tmpdir/'default.txt')
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if mode == 'path':
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new = Table.from_ASCII(tmpdir/'default.txt')
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elif mode == 'str':
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@ -43,19 +43,22 @@ class TestTable:
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assert all(default.data==new.data) and default.shapes == new.shapes
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def test_write_read_file(self,default,tmpdir):
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with open(tmpdir.join('default.txt'),'w') as f:
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default.to_ASCII(f)
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with open(tmpdir.join('default.txt')) as f:
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with open(tmpdir/'default.txt','w') as f:
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default.to_file(f)
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with open(tmpdir/'default.txt') as f:
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new = Table.from_ASCII(f)
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assert all(default.data==new.data) and default.shapes == new.shapes
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def test_write_read_new_style(self,default,tmpdir):
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with open(tmpdir.join('new_style.txt'),'w') as f:
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default.to_ASCII(f,new_style=True)
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with open(tmpdir.join('new_style.txt')) as f:
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with open(tmpdir/'new_style.txt','w') as f:
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default.to_file(f,new_style=True)
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with open(tmpdir/'new_style.txt') as f:
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new = Table.from_ASCII(f)
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assert all(default.data==new.data) and default.shapes == new.shapes
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def test_write_invalid_format(self,default,tmpdir):
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with pytest.raises(TypeError):
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default.to_file(tmpdir/'shouldnotbethere.txt',format='invalid')
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@pytest.mark.parametrize('mode',['str','path'])
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def test_read_ang(self,reference_dir,mode):
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