diff --git a/python/tamaas/dumpers/__init__.py b/python/tamaas/dumpers/__init__.py
index 5ac0b62..6bf3ab6 100644
--- a/python/tamaas/dumpers/__init__.py
+++ b/python/tamaas/dumpers/__init__.py
@@ -1,267 +1,285 @@
# -*- mode:python; coding: utf-8 -*-
# @file
# @section LICENSE
#
# Copyright (©) 2016-2020 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
"""
Dumpers for the class tamaas.Model
"""
from __future__ import print_function
from sys import stderr
from os import makedirs
import os.path
import numpy as np
from .. import ModelDumper, model_type
from ._helper import make_periodic, step_dump, directory_dump
class FieldDumper(ModelDumper):
"""Abstract dumper for python classes using fields"""
postfix = ''
extension = ''
name_format = "{basename}{postfix}.{extension}"
def __init__(self, basename, *fields, **kwargs):
"""Construct with desired fields"""
super(FieldDumper, self).__init__()
self.basename = basename
self.fields = fields
self.all_fields = kwargs.get('all_fields', False)
def add_field(self, field):
"""Add another field to the dump"""
if field not in self.fields:
self.fields.append(field)
def dump_to_file(self, fd, model):
"""Dump to a file (name or handle)"""
pass
def get_fields(self, model):
"""Get the desired fields"""
if not self.all_fields:
requested_fields = self.fields
else:
requested_fields = model.getFields()
return {field: model.getField(field) for field in requested_fields}
def get_attributes(self, model):
"""Get model attributes"""
return {
'model_type': str(model.type),
'system_size': model.getSystemSize(),
'discretization': model.getDiscretization()
}
def dump(self, model):
self.dump_to_file(self.file_path, model)
@property
def file_path(self):
"""Get the default filename"""
return self.name_format.format(basename=self.basename,
postfix=self.postfix,
extension=self.extension)
@directory_dump('numpys')
@step_dump
class NumpyDumper(FieldDumper):
"""Dumper to compressed numpy files"""
extension = 'npz'
def dump_to_file(self, fd, model):
"""Saving to compressed multi-field Numpy format"""
np.savez_compressed(fd, attrs=self.get_attributes(model),
**self.get_fields(model))
try:
import h5py
@directory_dump('hdf5')
@step_dump
class H5Dumper(FieldDumper):
"""Dumper to HDF5 file format"""
extension = 'h5'
def dump_to_file(self, fd, model):
"""Saving to HDF5 with metadata about the model"""
with h5py.File(fd, 'w') as fh:
# Writing data
for name, field in self.get_fields(model).items():
dset = fh.create_dataset(name, field.shape, field.dtype,
compression='gzip',
compression_opts=7)
dset[:] = field
# Writing metadata
for name, attr in self.get_attributes(model).items():
fh.attrs[name] = attr
except ImportError:
pass
try:
import uvw # noqa
@directory_dump('paraview')
@step_dump
class UVWDumper(FieldDumper):
"""Dumper to VTK files for elasto-plastic calculations"""
extension = 'vtr'
forbidden_fields = ['traction', 'gap'] # TODO make generic
def dump_to_file(self, fd, model):
"""Dump displacements, plastic deformations and stresses"""
discretization = model.getDiscretization().copy()
# Because we make fields periodic
discretization[1] += 1
discretization[2] += 1
# Space coordinates
coordinates = [np.linspace(0, L, N)
for L, N in zip(model.getSystemSize(),
discretization)]
# Correct order of coordinate dimensions
dimension_indices = [1, 2, 0]
# Creating rectilinear grid with correct order for components
grid = uvw.RectilinearGrid(
fd, (coordinates[i] for i in dimension_indices),
compression=True,
)
# Iterator over fields we want to dump
# Avoid 2D fields (TODO make generic)
fields_it = filter(lambda t: t[0] not in self.forbidden_fields,
self.get_fields(model).items())
# We make fields periodic for visualization
for name, field in fields_it:
array = uvw.DataArray(np.array(make_periodic[name](field),
dtype=np.double),
dimension_indices, name)
grid.addPointData(array)
grid.write()
@directory_dump('paraview')
class UVWGroupDumper(FieldDumper):
"Dumper to ParaViewData files"
extension = 'pvd'
def __init__(self, basename, *fields, **kwargs):
"""Construct with desired fields"""
super(UVWGroupDumper, self).__init__(basename, *fields, **kwargs)
subdir = os.path.join('paraview', basename + '-VTR')
if not os.path.exists(subdir):
makedirs(subdir)
self.uvw_dumper = UVWDumper(
os.path.join(basename + '-VTR', basename), *fields, **kwargs
)
self.group = uvw.ParaViewData(self.file_path, compression=True)
def dump_to_file(self, fd, model):
self.group.addFile(
self.uvw_dumper.file_path.replace('paraview/', ''),
timestep=self.uvw_dumper.count
)
self.group.write()
self.uvw_dumper.dump(model)
except ImportError as error:
print(error, file=stderr)
try:
from netCDF4 import Dataset
@directory_dump('netcdf')
- @step_dump
class NetCDFDumper(FieldDumper):
"""Dumper to netCDF4 files"""
extension = "nc"
boundary_fields = ['traction', 'gap']
- def dump_to_file(self, fd, model):
- with Dataset(fd, 'w', format='NETCDF4_CLASSIC') as rootgrp:
- model_dim = len(model.getDiscretization())
- self._vec = rootgrp.createDimension('spatial', model_dim)
- self._tens = rootgrp.createDimension('Voigt', 2*model_dim)
-
- self._dump_boundary(rootgrp, model)
+ def _file_setup(self, grp, model):
+ grp.createDimension('frame', None)
- if model.type in {model_type.volume_1d, model_type.volume_2d}:
- self._dump_volume(rootgrp, model)
+ # Local dimensions
+ model_dim = len(model.getDiscretization())
+ self._vec = grp.createDimension('spatial', model_dim)
+ self._tens = grp.createDimension('Voigt', 2*model_dim)
+ self.model_info = model.getDiscretization(), model.type
- def _dump_boundary(self, grp, model):
# Create boundary dimensions
it = zip("xy", model.getBoundaryDiscretization(),
- model.getSystemSize())
+ model.getBoundarySystemSize())
for label, size, length in it:
grp.createDimension(label, size)
coord = grp.createVariable(label, 'f8', (label,))
coord[:] = np.linspace(0, length, size, endpoint=False)
- self._dump_generic(grp, model,
- lambda f: f[0] in self.boundary_fields,
- 'boundary',
- model.getBoundaryDiscretization(),
- "xy")
+ self._create_variables(
+ grp, model,
+ lambda f: f[0] in self.boundary_fields,
+ model.getBoundaryDiscretization(), "xy"
+ )
- def _dump_volume(self, grp, model):
# Create volume dimension
- size = model.getDiscretization()[0]
- grp.createDimension("z", size)
- coord = grp.createVariable("z", 'f8', ("z",))
- coord[:] = np.linspace(0, model.getSystemSize()[0], size)
+ if model.type in {model_type.volume_1d, model_type.volume_2d}:
+ size = model.getDiscretization()[0]
+ grp.createDimension("z", size)
+ coord = grp.createVariable("z", 'f8', ("z",))
+ coord[:] = np.linspace(0, model.getSystemSize()[0], size)
+
+ self._create_variables(
+ grp, model,
+ lambda f: f[0] not in self.boundary_fields,
+ model.getDiscretization(), "zxy"
+ )
+
+ def dump_to_file(self, fd, model):
+ mode = 'a' if os.path.isfile(fd) else 'w'
- self._dump_generic(grp, model,
- lambda f: f[0] not in self.boundary_fields,
- 'volume', model.getDiscretization(), "zxy")
+ with Dataset(fd, mode, format='NETCDF4_CLASSIC') as rootgrp:
+ if rootgrp.dimensions == {}:
+ self._file_setup(rootgrp, model)
- def _dump_generic(self, grp, model, predicate,
- group_name, shape, dimensions):
+ if self.model_info != (model.getDiscretization(), model.type):
+ raise Exception("Unexpected model {}".format(model))
+
+ self._dump_generic(rootgrp, model)
+
+ def _create_variables(self, grp, model, predicate,
+ shape, dimensions):
field_dim = len(shape)
fields = filter(predicate, self.get_fields(model).items())
dim_labels = list(dimensions[:field_dim])
for label, data in fields:
dims = dim_labels
# If we have an extra component
if data.ndim > field_dim:
if data.shape[-1] == self._tens.size:
dims.append(self._tens.name)
elif data.shape[-1] == self._vec.size:
dims.append(self._vec.name)
- var = grp.createVariable(label, 'f8', dims)
- var[:] = np.array(data, dtype=np.double)
+ grp.createVariable(label, 'f8', ['frame'] + dims, zlib=True)
+
+ def _dump_generic(self, grp, model):
+ fields = self.get_fields(model).items()
+
+ new_frame = grp.dimensions['frame'].size
+ for label, data in fields:
+ var = grp[label]
+ var[new_frame, :] = np.array(data, dtype=np.double)
+
except ImportError:
pass
diff --git a/tests/test_dumper.py b/tests/test_dumper.py
index 393d66a..907a580 100644
--- a/tests/test_dumper.py
+++ b/tests/test_dumper.py
@@ -1,139 +1,148 @@
# -*- coding: utf-8 -*-
# @file
# @section LICENSE
#
# Copyright (©) 2016-2020 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
from __future__ import division
import os
import shutil
import tamaas as tm
import numpy as np
import warnings
warnings.filterwarnings('ignore')
+import pytest
from tamaas.dumpers import NumpyDumper
class Dumper(tm.ModelDumper):
"""Simple numpy dumper"""
def __init__(self):
tm.ModelDumper.__init__(self)
def dump(self, model):
np.savetxt('tractions.txt', np.ravel(model.getField('traction')))
np.savetxt('displacement.txt',
np.ravel(model.getField('displacement')))
def cleanup():
for name in ['tractions.txt',
'displacement.txt',
'numpys',
'hdf5',
'netcdf']:
if os.path.exists(name) and os.path.isdir(name):
shutil.rmtree(name)
elif os.path.exists(name):
os.remove(name)
def test_dumpers(tamaas_fixture):
model = tm.ModelFactory.createModel(tm.model_type.volume_2d, [1., 1., 1.],
[16, 4, 8])
dumper = Dumper()
np_dumper = NumpyDumper('test_dump', 'traction', 'displacement')
model.addDumper(np_dumper)
model.dump()
model.dump()
dumper << model
ref_t = model.getTraction()
ref_d = model.getDisplacement()
tractions = np.loadtxt('tractions.txt')
displacements = np.loadtxt('displacement.txt')
assert np.all(tractions.reshape(ref_t.shape) == ref_t)
assert np.all(displacements.reshape(ref_d.shape) == ref_d)
with np.load('numpys/test_dump_0000.npz', allow_pickle=True) as npfile:
tractions = npfile['traction']
displacements = npfile['displacement']
attributes = npfile['attrs'].item()
assert np.all(tractions == ref_t)
assert np.all(displacements == ref_d)
assert str(model.type) == attributes['model_type']
assert os.path.isfile('numpys/test_dump_0001.npz')
cleanup()
# Protecting test
try:
from tamaas.dumpers import H5Dumper
import h5py
def test_h5dumper(tamaas_fixture):
model = tm.ModelFactory.createModel(tm.model_type.volume_2d,
[1., 1., 1.],
[16, 4, 8])
model.getDisplacement()[...] = 3.1415
dumper = H5Dumper('test_hdf5', 'traction', 'displacement')
dumper << model
assert os.path.isfile('hdf5/test_hdf5_0000.h5')
fh = h5py.File('hdf5/test_hdf5_0000.h5', 'r')
disp = np.array(fh['displacement'], dtype=tm.dtype)
assert np.all(np.abs(disp - 3.1415) < 1e-15)
assert list(fh.attrs['discretization']) == [16, 4, 8]
assert fh.attrs['model_type'] == str(model.type)
fh.close()
cleanup()
except ImportError:
pass
try:
from tamaas.dumpers import NetCDFDumper
- import netCDF4
+ from netCDF4 import Dataset
def test_netcdfdumper(tamaas_fixture):
model = tm.ModelFactory.createModel(tm.model_type.volume_2d,
[1., 1., 1.],
[16, 4, 8])
model.getDisplacement()[...] = 3.1415
dumper = NetCDFDumper('test_netcdf', 'traction', 'displacement')
+ # Dumping two frames
+ dumper << model
dumper << model
- assert os.path.isfile('netcdf/test_netcdf_0000.nc')
+ assert os.path.isfile('netcdf/test_netcdf.nc')
- fh = netCDF4.Dataset('netcdf/test_netcdf_0000.nc', 'r')
- disp = fh['displacement'][:]
- assert np.all(np.abs(disp - 3.1415) < 1e-15)
- assert disp.shape == (16, 4, 8, 3)
+ with Dataset('netcdf/test_netcdf.nc', 'r') as netcdf_file:
+ disp = netcdf_file['displacement'][:]
+ assert np.all(np.abs(disp - 3.1415) < 1e-15)
+ assert disp.shape[1:] == (16, 4, 8, 3)
+ assert disp.shape[0] == 2
+
+ with pytest.raises(Exception):
+ model = tm.ModelFactory.createModel(tm.model_type.volume_2d,
+ [1., 1., 1.],
+ [15, 4, 8])
+ dumper << model
- fh.close()
cleanup()
except ImportError:
pass