158 lines
6.1 KiB
Python
158 lines
6.1 KiB
Python
# -*- coding: UTF-8 no BOM -*-
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import h5py
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import re
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import numpy as np
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# ------------------------------------------------------------------
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class DADF5():
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"""Read and write to DADF5 files"""
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# ------------------------------------------------------------------
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def __init__(self,
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filename,
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mode = 'r',
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):
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if mode not in ['a','r']:
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print('Invalid file access mode')
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with h5py.File(filename,mode):
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pass
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with h5py.File(filename,'r') as f:
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if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 2:
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raise TypeError('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version']))
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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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r=re.compile('inc[0-9]+')
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self.increments = [{'inc': int(u[3:]),
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'time': round(f[u].attrs['time/s'],12),
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} for u in f.keys() if r.match(u)]
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self.constituents = np.unique(f['mapping/cellResults/constituent']['Name']).tolist() # ToDo: I am not to happy with the name
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self.constituents = [c.decode() for c in self.constituents]
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self.materialpoints = np.unique(f['mapping/cellResults/materialpoint']['Name']).tolist() # ToDo: I am not to happy with the name
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self.materialpoints = [m.decode() for m in self.materialpoints]
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self.Nconstituents = [i for i in range(np.shape(f['mapping/cellResults/constituent'])[1])]
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self.Nmaterialpoints = np.shape(f['mapping/cellResults/constituent'])[0]
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self.c_output_types = []
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for c in self.constituents:
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for o in f['inc{:05}/constituent/{}'.format(self.increments[0]['inc'],c)].keys():
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self.c_output_types.append(o)
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self.c_output_types = list(set(self.c_output_types)) # make unique
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self.m_output_types = []
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for m in self.materialpoints:
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for o in f['inc{:05}/materialpoint/{}'.format(self.increments[0]['inc'],m)].keys():
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self.m_output_types.append(o)
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self.m_output_types = list(set(self.m_output_types)) # make unique
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self.active= {'increments': self.increments,
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'constituents': self.constituents,
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'materialpoints': self.materialpoints,
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'constituent': self.Nconstituents,
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'c_output_types': self.c_output_types,
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'm_output_types': self.m_output_types}
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self.filename = filename
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self.mode = mode
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def list_data(self):
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"""Shows information on all datasets in the file"""
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with h5py.File(self.filename,'r') as f:
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group_inc = 'inc{:05}'.format(self.active['increments'][0]['inc'])
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for c in self.active['constituents']:
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print('\n'+c)
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group_constituent = group_inc+'/constituent/'+c
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for t in self.active['c_output_types']:
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print(' {}'.format(t))
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group_output_types = group_constituent+'/'+t
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try:
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for x in f[group_output_types].keys():
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print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
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except:
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pass
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for m in self.active['materialpoints']:
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group_materialpoint = group_inc+'/materialpoint/'+m
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for t in self.active['m_output_types']:
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print(' {}'.format(t))
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group_output_types = group_materialpoint+'/'+t
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try:
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for x in f[group_output_types].keys():
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print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
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except:
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pass
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def get_dataset_location(self,label):
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"""Returns the location of all active datasets with given label"""
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path = []
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with h5py.File(self.filename,'r') as f:
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for i in self.active['increments']:
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group_inc = 'inc{:05}'.format(i['inc'])
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for c in self.active['constituents']:
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group_constituent = group_inc+'/constituent/'+c
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for t in self.active['c_output_types']:
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try:
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f[group_constituent+'/'+t+'/'+label]
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path.append(group_constituent+'/'+t+'/'+label)
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except Exception as e:
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print('unable to locate constituents dataset: '+ str(e))
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for m in self.active['materialpoints']:
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group_materialpoint = group_inc+'/materialpoint/'+m
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for t in self.active['m_output_types']:
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try:
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f[group_materialpoint+'/'+t+'/'+label]
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path.append(group_materialpoint+'/'+t+'/'+label)
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except Exception as e:
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print('unable to locate materialpoints dataset: '+ str(e))
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return path
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def read_dataset(self,path,c):
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"""
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Dataset for all points/cells
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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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with h5py.File(self.filename,'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)
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for pa in path:
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label = pa.split('/')[2]
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try:
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p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
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u = (f['mapping/cellResults/constituent'][p,c]['Position'])
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a = np.array(f[pa])
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if len(a.shape) == 1:
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a=a.reshape([a.shape[0],1])
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dataset[p,:] = a[u,:]
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except Exception as e:
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print('unable to read constituent: '+ str(e))
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try:
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p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
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u = (f['mapping/cellResults/materialpoint'][p.tolist()]['Position'])
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a = np.array(f[pa])
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if len(a.shape) == 1:
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a=a.reshape([a.shape[0],1])
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dataset[p,:] = a[u,:]
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except Exception as e:
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print('unable to read materialpoint: '+ str(e))
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return dataset
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