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Merge branch 'PythonImprovements' into pytest

This commit is contained in:
Martin Diehl 2019-11-25 09:15:06 +01:00
parent 928a5c2e55 3e8518d861
commit 969fa9bbc7
21 changed files with 135 additions and 158 deletions
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4
processing/post/DADF5_postResults.py
View File

@ -65,7 +65,7 @@ for filename in options.filenames:
x = results.get_dataset_location(label)
if len(x) == 0:
continue
array = results.read_dataset(x,0)
array = results.read_dataset(x,0,plain=True)
d = int(np.product(np.shape(array)[1:]))
data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
@ -80,7 +80,7 @@ for filename in options.filenames:
x = results.get_dataset_location(label)
if len(x) == 0:
continue
array = results.read_dataset(x,0)
array = results.read_dataset(x,0,plain=True)
d = int(np.product(np.shape(array)[1:]))
data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)

5
processing/pre/geom_addPrimitive.py
View File

@ -132,7 +132,4 @@ for name in filenames:
damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

7
processing/pre/geom_canvas.py
View File

@ -61,7 +61,7 @@ for name in filenames:
canvas = np.full(new,options.fill if options.fill is not None
else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
l = np.clip( offset, 0,np.minimum(old +offset,new))
l = np.clip( offset, 0,np.minimum(old +offset,new)) # noqa
r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
L = np.clip(-offset, 0,np.minimum(new -offset,old))
R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
@ -71,7 +71,4 @@ for name in filenames:
damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

11
processing/pre/geom_clean.py
View File

@ -5,9 +5,6 @@ import sys
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import numpy as np
import damask
@ -40,12 +37,6 @@ for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom.clean(options.stencil))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

14
processing/pre/geom_fromDREAM3D.py
View File

@ -86,7 +86,7 @@ for name in filenames:
* inFile[os.path.join(group_geom,'SPACING')][...]
grid = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
except:
except KeyError:
errors.append('Geometry data ({}) not found'.format(group_geom))
@ -98,13 +98,13 @@ for name in filenames:
try:
quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
except:
except KeyError:
errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
dataset = os.path.join(group_pointwise,options.phase)
try:
phase = np.reshape(inFile[dataset][...],(np.product(grid)))
except:
except KeyError:
errors.append('Pointwise phase data ({}) not readable'.format(dataset))
microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
@ -116,7 +116,7 @@ for name in filenames:
dataset = os.path.join(group_pointwise,options.microstructure)
try:
microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
except:
except KeyError:
errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
group_average = os.path.join(rootDir,options.basegroup,options.average)
@ -124,13 +124,13 @@ for name in filenames:
dataset = os.path.join(group_average,options.quaternion)
try:
rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
except:
except KeyError:
errors.append('Average orientation data ({}) not readable'.format(dataset))
dataset = os.path.join(group_average,options.phase)
try:
phase = [i[0] for i in inFile[dataset][...]][1:] # skip first entry (unindexed)
except:
except KeyError:
errors.append('Average phase data ({}) not readable'.format(dataset))
if errors != []:
@ -155,4 +155,4 @@ for name in filenames:
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
geom.to_file(os.path.splitext(name)[0]+'.geom')
geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False)

5
processing/pre/geom_fromMinimalSurface.py
View File

@ -89,7 +89,4 @@ geom=damask.Geom(microstructure,options.size,
comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_fromOsteonGeometry.py
View File

@ -145,7 +145,4 @@ geom = damask.Geom(microstructure.reshape(grid),
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_fromScratch.py
View File

@ -63,7 +63,4 @@ geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype)
comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_fromTable.py
View File

@ -152,7 +152,4 @@ for name in filenames:
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(os.path.splitext(name)[0]+'.geom')
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)

5
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -302,7 +302,4 @@ for name in filenames:
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(os.path.splitext(name)[0]+'.geom')
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)

5
processing/pre/geom_grainGrowth.py
View File

@ -172,7 +172,4 @@ for name in filenames:
damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

9
processing/pre/geom_mirror.py
View File

@ -5,8 +5,6 @@ import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
@ -44,11 +42,6 @@ for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom.mirror(options.directions,options.reflect))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

39
processing/pre/geom_pack.py
View File

@ -34,41 +34,4 @@ for name in filenames:
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
compressType = None
former = start = -1
reps = 0
if name is None:
f = sys.stdout
else:
f= open(name,'w')
for current in geom.microstructure.flatten('F'):
if abs(current - former) == 1 and (start - current) == reps*(former - current):
compressType = 'to'
reps += 1
elif current == former and start == former:
compressType = 'of'
reps += 1
else:
if compressType is None:
f.write('\n'.join(geom.get_header())+'\n')
elif compressType == '.':
f.write('{}\n'.format(former))
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))
compressType = '.'
start = current
reps = 1
former = current
if compressType == '.':
f.write('{}\n'.format(former))
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))
geom.to_file(sys.stdout if name is None else name,pack=True)

15
processing/pre/geom_renumber.py
View File

@ -5,8 +5,6 @@ import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
@ -32,15 +30,6 @@ for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
for i, oldID in enumerate(np.unique(geom.microstructure)):
renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)
damask.util.croak(geom.update(renumbered))
damask.util.croak(geom.renumber)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

24
processing/pre/geom_rescale.py
View File

@ -2,11 +2,10 @@
import os
import sys
import numpy as np
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import numpy as np
import damask
@ -55,20 +54,7 @@ for name in filenames:
np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \
else float(n) for o,n in zip(size,options.size)],dtype=float)
damask.util.croak(geom.update(microstructure =
ndimage.interpolation.zoom(
geom.microstructure,
new_grid/grid,
output=geom.microstructure.dtype,
order=0,
mode='nearest',
prefilter=False,
) if np.any(new_grid != grid) \
else None,
size = new_size))
geom.scale(new_grid)
damask.util.croak(geom.update(microstructure = None,size = new_size))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_rotate.py
View File

@ -95,7 +95,4 @@ for name in filenames:
damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_translate.py
View File

@ -58,7 +58,4 @@ for name in filenames:
damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_unpack.py
View File

@ -34,7 +34,4 @@ for name in filenames:
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
processing/pre/geom_vicinityOffset.py
View File

@ -82,7 +82,4 @@ for name in filenames:
geom.microstructure + offset,geom.microstructure)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)
geom.to_file(sys.stdout if name is None else name,pack=False)

5
python/damask/dadf5.py
View File

@ -369,7 +369,7 @@ class DADF5():
return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string
def read_dataset(self,path,c):
def read_dataset(self,path,c=0,plain=False):
"""
Dataset for all points/cells.
@ -402,6 +402,9 @@ class DADF5():
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

98
python/damask/geom.py
View File

@ -299,7 +299,7 @@ class Geom():
return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
def to_file(self,fname):
def to_file(self,fname,pack=None):
"""
Writes a geom file.
@ -307,15 +307,63 @@ class Geom():
----------
fname : str or file handle
geometry file to write.
pack : bool, optional
compress geometry with 'x of y' and 'a to b'.
"""
header = self.get_header()
grid = self.get_grid()
format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
else '%g'
if pack is None:
plain = grid.prod()/np.unique(self.microstructure).size < 250
else:
plain = not pack
if plain:
format_string = '%g' if self.microstructure in np.sctypes['float'] else \
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
np.savetxt(fname,
self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
else:
if isinstance(fname,str):
f = open(fname,'w')
else:
f = fname
compressType = None
former = start = -1
reps = 0
for current in self.microstructure.flatten('F'):
if abs(current - former) == 1 and (start - current) == reps*(former - current):
compressType = 'to'
reps += 1
elif current == former and start == former:
compressType = 'of'
reps += 1
else:
if compressType is None:
f.write('\n'.join(self.get_header())+'\n')
elif compressType == '.':
f.write('{}\n'.format(former))
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))
compressType = '.'
start = current
reps = 1
former = current
if compressType == '.':
f.write('{}\n'.format(former))
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))
def to_vtk(self,fname=None):
"""
@ -390,12 +438,14 @@ class Geom():
def mirror(self,directions,reflect=False):
"""
Mirror microstructure along given directions.
Parameters
----------
directions : iterable containing str
direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
reflect : bool, optional
reflect (include) outermost layers.
"""
valid = {'x','y','z'}
if not all(isinstance(d, str) for d in directions):
@ -417,19 +467,57 @@ class Geom():
#self.add_comments('tbd')
def scale(self,grid):
"""
Scale microstructure to new grid.
Parameters
----------
grid : iterable of int
new grid dimension
"""
return self.update(
ndimage.interpolation.zoom(
self.microstructure,
grid/self.get_grid(),
output=self.microstructure.dtype,
order=0,
mode='nearest',
prefilter=False
)
)
#self.add_comments('tbd')
def clean(self,stencil=3):
"""
Smooth microstructure by selecting most frequent index within given stencil at each location.
Parameters
----------
stencil : int, optional
size of smoothing stencil.
"""
def mostFrequent(arr):
unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))]
return self.update(ndimage.filters.generic_filter(self.microstructure,
return self.update(ndimage.filters.generic_filter(
self.microstructure,
mostFrequent,
size=(stencil,)*3).astype(self.microstructure.dtype))
size=(stencil,)*3
).astype(self.microstructure.dtype)
)
#self.add_comments('tbd')
def renumber(self):
"""Renumber sorted microstructure indices to 1,...,N."""
renumbered = np.empty(self.get_grid(),dtype=self.microstructure.dtype)
for i, oldID in enumerate(np.unique(self.microstructure)):
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
return self.update(renumbered)
#self.add_comments('tbd')