4 space indentation
This commit is contained in:
Martin Diehl
parent
76caf422aa
commit
1e178287fe
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@ -37,43 +37,43 @@ class Result:
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"""
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"""
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with h5py.File(fname,'r') as f:
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with h5py.File(fname,'r') as f:
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try:
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try:
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self.version_major = f.attrs['DADF5_version_major']
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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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self.version_minor = f.attrs['DADF5_version_minor']
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except KeyError:
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except KeyError:
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self.version_major = f.attrs['DADF5-major']
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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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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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if self.version_major != 0 or not 2 <= self.version_minor <= 6:
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raise TypeError('Unsupported DADF5 version {}.{} '.format(self.version_major,
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raise TypeError('Unsupported DADF5 version {}.{} '.format(self.version_major,
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self.version_minor))
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self.version_minor))
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self.structured = 'grid' in f['geometry'].attrs.keys()
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self.structured = 'grid' in f['geometry'].attrs.keys()
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if self.structured:
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if self.structured:
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self.grid = f['geometry'].attrs['grid']
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self.grid = f['geometry'].attrs['grid']
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self.size = f['geometry'].attrs['size']
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self.size = f['geometry'].attrs['size']
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self.origin = f['geometry'].attrs['origin'] if self.version_major == 0 and self.version_minor >= 5 else \
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self.origin = f['geometry'].attrs['origin'] if self.version_major == 0 and self.version_minor >= 5 else \
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np.zeros(3)
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np.zeros(3)
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r=re.compile('inc[0-9]+')
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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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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.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.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.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.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.constituents = [c.decode() for c in np.unique(f['mapping/cellResults/constituent'] ['Name'])]
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self.con_physics = []
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self.con_physics = []
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for c in self.constituents:
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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 += 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.con_physics = list(set(self.con_physics)) # make unique
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self.mat_physics = []
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self.mat_physics = []
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for m in self.materialpoints:
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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 += 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.mat_physics = list(set(self.mat_physics)) # make unique
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self.selection= {'increments': self.increments,
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self.selection= {'increments': self.increments,
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'constituents': self.constituents,'materialpoints': self.materialpoints,
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'constituents': self.constituents,'materialpoints': self.materialpoints,
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@ -343,14 +343,14 @@ class Result:
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with h5py.File(self.fname,'r') as f:
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with h5py.File(self.fname,'r') as f:
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for i in self.iterate('increments'):
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for i in self.iterate('increments'):
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for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for oo in self.iterate(o):
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for oo in self.iterate(o):
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for pp in self.iterate(p):
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for pp in self.iterate(p):
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group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue
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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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if sets is True:
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groups.append(group)
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groups.append(group)
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else:
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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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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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if len(set(match)) == len(sets) : groups.append(group)
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return groups
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return groups
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@ -361,18 +361,18 @@ class Result:
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for i in self.iterate('increments'):
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for i in self.iterate('increments'):
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message+='\n{} ({}s)\n'.format(i,self.times[self.increments.index(i)])
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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 o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for oo in self.iterate(o):
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for oo in self.iterate(o):
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message+=' {}\n'.format(oo)
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message+=' {}\n'.format(oo)
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for pp in self.iterate(p):
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for pp in self.iterate(p):
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message+=' {}\n'.format(pp)
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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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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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for d in f[group].keys():
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try:
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try:
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dataset = f['/'.join([group,d])]
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dataset = f['/'.join([group,d])]
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message+=' {} / ({}): {}\n'.\
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message+=' {} / ({}): {}\n'.\
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format(d,dataset.attrs['Unit'].decode(),dataset.attrs['Description'].decode())
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format(d,dataset.attrs['Unit'].decode(),dataset.attrs['Description'].decode())
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except KeyError:
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except KeyError:
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pass
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pass
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return message
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return message
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@ -385,7 +385,7 @@ class Result:
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try:
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try:
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f[k]
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f[k]
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path.append(k)
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path.append(k)
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except KeyError as e:
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except KeyError:
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pass
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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 o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
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for oo in self.iterate(o):
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for oo in self.iterate(o):
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@ -394,7 +394,7 @@ class Result:
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try:
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try:
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f[k]
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f[k]
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path.append(k)
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path.append(k)
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except KeyError as e:
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except KeyError:
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pass
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pass
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return path
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return path
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@ -419,31 +419,31 @@ class Result:
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If more than one path is given, the dataset is composed of the individual contributions.
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If more than one path is given, the dataset is composed of the individual contributions.
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"""
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"""
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with h5py.File(self.fname,'r') as f:
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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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shape = (self.Nmaterialpoints,) + np.shape(f[path[0]])[1:]
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if len(shape) == 1: shape = shape +(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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dataset = np.full(shape,np.nan,dtype=np.dtype(f[path[0]]))
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for pa in path:
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for pa in path:
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label = pa.split('/')[2]
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label = pa.split('/')[2]
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if (pa.split('/')[1] == 'geometry'):
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if (pa.split('/')[1] == 'geometry'):
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dataset = np.array(f[pa])
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dataset = np.array(f[pa])
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continue
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continue
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p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
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p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
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if len(p)>0:
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if len(p)>0:
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u = (f['mapping/cellResults/constituent']['Position'][p,c])
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u = (f['mapping/cellResults/constituent']['Position'][p,c])
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a = np.array(f[pa])
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a = np.array(f[pa])
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if len(a.shape) == 1:
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if len(a.shape) == 1:
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a=a.reshape([a.shape[0],1])
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a=a.reshape([a.shape[0],1])
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dataset[p,:] = a[u,:]
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dataset[p,:] = a[u,:]
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p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
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p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
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if len(p)>0:
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if len(p)>0:
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u = (f['mapping/cellResults/materialpoint']['Position'][p.tolist()])
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u = (f['mapping/cellResults/materialpoint']['Position'][p.tolist()])
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a = np.array(f[pa])
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a = np.array(f[pa])
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if len(a.shape) == 1:
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if len(a.shape) == 1:
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a=a.reshape([a.shape[0],1])
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a=a.reshape([a.shape[0],1])
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dataset[p,:] = a[u,:]
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dataset[p,:] = a[u,:]
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if plain and dataset.dtype.names is not None:
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if plain and dataset.dtype.names is not None:
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return dataset.view(('float64',len(dataset.dtype.names)))
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return dataset.view(('float64',len(dataset.dtype.names)))
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@ -518,7 +518,7 @@ class Result:
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"""
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"""
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if not vectorized:
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if not vectorized:
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raise NotImplementedError
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raise NotImplementedError
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dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
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dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
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args = {'formula':formula,'label':label,'unit':unit,'description':description}
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args = {'formula':formula,'label':label,'unit':unit,'description':description}
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@ -661,9 +661,9 @@ class Result:
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lattice = q['meta']['Lattice']
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lattice = q['meta']['Lattice']
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for i,q in enumerate(q['data']):
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for i,qu in enumerate(q['data']):
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o = Orientation(np.array([q['w'],q['x'],q['y'],q['z']]),lattice).reduced()
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o = Orientation(np.array([qu['w'],qu['x'],qu['y'],qu['z']]),lattice).reduced()
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colors[i] = np.uint8(o.IPFcolor(d_unit)*255)
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colors[i] = np.uint8(o.IPFcolor(d_unit)*255)
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return {
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return {
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'data': colors,
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'data': colors,
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m = util.scale_to_coprime(pole)
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m = util.scale_to_coprime(pole)
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coords = np.empty((len(q['data']),2))
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coords = np.empty((len(q['data']),2))
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for i,q in enumerate(q['data']):
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for i,qu in enumerate(q['data']):
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o = Rotation(np.array([q['w'],q['x'],q['y'],q['z']]))
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o = Rotation(np.array([qu['w'],qu['x'],qu['y'],qu['z']]))
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rotatedPole = o*unit_pole # rotate pole according to crystal orientation
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rotatedPole = o*unit_pole # rotate pole according to crystal orientation
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(x,y) = rotatedPole[0:2]/(1.+abs(unit_pole[2])) # stereographic projection
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(x,y) = rotatedPole[0:2]/(1.+abs(unit_pole[2])) # stereographic projection
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coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y]
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coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y]
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@ -1036,67 +1036,67 @@ class Result:
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"""
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"""
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if mode.lower()=='cell':
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if mode.lower()=='cell':
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if self.structured:
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if self.structured:
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v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
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v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
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else:
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else:
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with h5py.File(self.fname,'r') as f:
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with h5py.File(self.fname,'r') as f:
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v = VTK.from_unstructuredGrid(f['/geometry/x_n'][()],
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v = VTK.from_unstructuredGrid(f['/geometry/x_n'][()],
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f['/geometry/T_c'][()]-1,
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f['/geometry/T_c'][()]-1,
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f['/geometry/T_c'].attrs['VTK_TYPE'].decode())
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f['/geometry/T_c'].attrs['VTK_TYPE'].decode())
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elif mode.lower()=='point':
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elif mode.lower()=='point':
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v = VTK.from_polyData(self.cell_coordinates())
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v = VTK.from_polyData(self.cell_coordinates())
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N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
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N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
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for i,inc in enumerate(util.show_progress(self.iterate('increments'),len(self.selection['increments']))):
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for inc in util.show_progress(self.iterate('increments'),len(self.selection['increments'])):
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materialpoints_backup = self.selection['materialpoints'].copy()
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materialpoints_backup = self.selection['materialpoints'].copy()
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self.pick('materialpoints',False)
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self.pick('materialpoints',False)
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for label in (labels if isinstance(labels,list) else [labels]):
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for label in (labels if isinstance(labels,list) else [labels]):
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for p in self.iterate('con_physics'):
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for p in self.iterate('con_physics'):
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if p != 'generic':
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if p != 'generic':
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for c in self.iterate('constituents'):
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for c in self.iterate('constituents'):
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x = self.get_dataset_location(label)
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x = self.get_dataset_location(label)
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if len(x) == 0:
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if len(x) == 0:
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continue
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continue
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array = self.read_dataset(x,0)
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array = self.read_dataset(x,0)
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v.add(array,'1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
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v.add(array,'1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
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else:
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else:
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x = self.get_dataset_location(label)
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x = self.get_dataset_location(label)
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if len(x) == 0:
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if len(x) == 0:
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continue
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continue
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array = self.read_dataset(x,0)
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array = self.read_dataset(x,0)
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ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name
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ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name
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dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name
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dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name
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v.add(array,dset_name)
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v.add(array,dset_name)
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self.pick('materialpoints',materialpoints_backup)
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self.pick('materialpoints',materialpoints_backup)
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constituents_backup = self.selection['constituents'].copy()
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constituents_backup = self.selection['constituents'].copy()
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self.pick('constituents',False)
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self.pick('constituents',False)
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for label in (labels if isinstance(labels,list) else [labels]):
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for label in (labels if isinstance(labels,list) else [labels]):
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for p in self.iterate('mat_physics'):
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for p in self.iterate('mat_physics'):
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if p != 'generic':
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if p != 'generic':
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for m in self.iterate('materialpoints'):
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for m in self.iterate('materialpoints'):
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x = self.get_dataset_location(label)
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x = self.get_dataset_location(label)
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if len(x) == 0:
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if len(x) == 0:
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continue
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continue
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array = self.read_dataset(x,0)
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array = self.read_dataset(x,0)
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v.add(array,'1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
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v.add(array,'1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
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else:
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else:
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x = self.get_dataset_location(label)
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x = self.get_dataset_location(label)
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if len(x) == 0:
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if len(x) == 0:
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continue
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continue
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array = self.read_dataset(x,0)
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array = self.read_dataset(x,0)
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v.add(array,'1_'+x[0].split('/',1)[1])
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v.add(array,'1_'+x[0].split('/',1)[1])
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self.pick('constituents',constituents_backup)
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self.pick('constituents',constituents_backup)
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u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
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u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
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v.add(u,'u')
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v.add(u,'u')
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file_out = '{}_inc{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
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file_out = '{}_inc{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
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inc[3:].zfill(N_digits))
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inc[3:].zfill(N_digits))
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||||||
v.write(file_out)
|
v.write(file_out)
|
||||||
|
|
||||||
###################################################################################################
|
###################################################################################################
|
||||||
# BEGIN DEPRECATED
|
# BEGIN DEPRECATED
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue