From a0504f51e60d1b447b42e525f52e8dc1ae3d03fc Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Wed, 6 Mar 2019 13:15:50 +0100
Subject: [PATCH] update reading of hdf5 dataset values
.value was deprecated, so I now use [...], which should work for old
enough versions (they recommend [()] instead).
---
bfps/DNS.py | 28 ++++++++++++++--------------
bfps/PP.py | 26 +++++++++++++-------------
bfps/_base.py | 4 ++--
bfps/_code.py | 2 +-
bfps/test/test_bfps_NSVEparticles.py | 12 ++++++------
bfps/test/test_bfps_resize.py | 4 ++--
bfps/test/test_fftw.py | 4 ++--
bfps/test/test_interpolation.py | 8 ++++----
bfps/test/test_particle_clouds.py | 16 ++++++++--------
bfps/test/test_particles.py | 12 ++++++------
bfps/tools.py | 16 ++++++++--------
tests/test_field_class.py | 6 +++---
tests/test_filters.py | 10 +++++-----
tests/test_particles.py | 4 ++--
14 files changed, 76 insertions(+), 76 deletions(-)
diff --git a/bfps/DNS.py b/bfps/DNS.py
index e0d83caf..6cc994ca 100644
--- a/bfps/DNS.py
+++ b/bfps/DNS.py
@@ -235,11 +235,11 @@ class DNS(_code):
'vel_max(t)',
'renergy(t)']:
if k in pp_file.keys():
- self.statistics[k] = pp_file[k].value
- self.statistics['kM'] = pp_file['kspace/kM'].value
- self.statistics['dk'] = pp_file['kspace/dk'].value
- self.statistics['kshell'] = pp_file['kspace/kshell'].value
- self.statistics['nshell'] = pp_file['kspace/nshell'].value
+ self.statistics[k] = pp_file[k][...]
+ self.statistics['kM'] = pp_file['kspace/kM'][...]
+ self.statistics['dk'] = pp_file['kspace/dk'][...]
+ self.statistics['kshell'] = pp_file['kspace/kshell'][...]
+ self.statistics['nshell'] = pp_file['kspace/nshell'][...]
else:
self.read_parameters()
with self.get_data_file() as data_file:
@@ -249,26 +249,26 @@ class DNS(_code):
self.parameters['niter_stat']-1),
iter0)
if type(iter1) == type(None):
- iter1 = data_file['iteration'].value
+ iter1 = data_file['iteration'][...]
else:
- iter1 = min(data_file['iteration'].value, iter1)
+ iter1 = min(data_file['iteration'][...], iter1)
ii0 = iter0 // self.parameters['niter_stat']
ii1 = iter1 // self.parameters['niter_stat']
- self.statistics['kshell'] = data_file['kspace/kshell'].value
- self.statistics['nshell'] = data_file['kspace/nshell'].value
+ self.statistics['kshell'] = data_file['kspace/kshell'][...]
+ self.statistics['nshell'] = data_file['kspace/nshell'][...]
for kk in [-1, -2]:
if (self.statistics['kshell'][kk] == 0):
self.statistics['kshell'][kk] = np.nan
- self.statistics['kM'] = data_file['kspace/kM'].value
- self.statistics['dk'] = data_file['kspace/dk'].value
+ self.statistics['kM'] = data_file['kspace/kM'][...]
+ self.statistics['dk'] = data_file['kspace/dk'][...]
computation_needed = True
pp_file = h5py.File(self.get_postprocess_file_name(), 'a')
if not ('parameters' in pp_file.keys()):
data_file.copy('parameters', pp_file)
data_file.copy('kspace', pp_file)
if 'ii0' in pp_file.keys():
- computation_needed = not (ii0 == pp_file['ii0'].value and
- ii1 == pp_file['ii1'].value)
+ computation_needed = not (ii0 == pp_file['ii0'][...] and
+ ii1 == pp_file['ii1'][...])
if computation_needed:
for k in ['t', 'vel_max(t)', 'renergy(t)',
'energy(t)', 'enstrophy(t)',
@@ -312,7 +312,7 @@ class DNS(_code):
'vel_max(t)',
'renergy(t)']:
if k in pp_file.keys():
- self.statistics[k] = pp_file[k].value
+ self.statistics[k] = pp_file[k][...]
# sanity check --- Parseval theorem check
assert(np.max(np.abs(
self.statistics['renergy(t)'] -
diff --git a/bfps/PP.py b/bfps/PP.py
index 77bf9d6c..72e693d4 100644
--- a/bfps/PP.py
+++ b/bfps/PP.py
@@ -184,19 +184,19 @@ class PP(_code):
self.parameters['niter_stat']-1),
iter0)
if type(iter1) == type(None):
- iter1 = data_file['iteration'].value
+ iter1 = data_file['iteration'][...]
else:
- iter1 = min(data_file['iteration'].value, iter1)
+ iter1 = min(data_file['iteration'][...], iter1)
ii0 = iter0 // self.parameters['niter_stat']
ii1 = iter1 // self.parameters['niter_stat']
- self.statistics['kshell'] = data_file['kspace/kshell'].value
- self.statistics['kM'] = data_file['kspace/kM'].value
- self.statistics['dk'] = data_file['kspace/dk'].value
+ self.statistics['kshell'] = data_file['kspace/kshell'][...]
+ self.statistics['kM'] = data_file['kspace/kM'][...]
+ self.statistics['dk'] = data_file['kspace/dk'][...]
computation_needed = True
pp_file = h5py.File(self.get_postprocess_file_name(), 'a')
if 'ii0' in pp_file.keys():
- computation_needed = not (ii0 == pp_file['ii0'].value and
- ii1 == pp_file['ii1'].value)
+ computation_needed = not (ii0 == pp_file['ii0'][...] and
+ ii1 == pp_file['ii1'][...])
if computation_needed:
for k in pp_file.keys():
del pp_file[k]
@@ -224,7 +224,7 @@ class PP(_code):
'vel_max(t)',
'renergy(t)']:
if k in pp_file.keys():
- self.statistics[k] = pp_file[k].value
+ self.statistics[k] = pp_file[k][...]
self.compute_time_averages()
return None
def compute_time_averages(self):
@@ -503,7 +503,7 @@ class PP(_code):
for k in self.pp_parameters.keys():
self.parameters[k] = self.pp_parameters[k]
self.pars_from_namespace(opt)
- niter_out = self.get_data_file()['parameters/niter_out'].value
+ niter_out = self.get_data_file()['parameters/niter_out'][...]
assert(opt.iter0 % niter_out == 0)
self.pp_parameters['iteration_list'] = np.arange(
opt.iter0, opt.iter1+niter_out, niter_out, dtype = np.int)
@@ -672,7 +672,7 @@ class PP(_code):
parameters = self.pp_parameters,
get_sim_info = False)
for kk in ['nx', 'ny', 'nz']:
- self.parameters[kk] = self.get_data_file()['parameters/' + kk].value
+ self.parameters[kk] = self.get_data_file()['parameters/' + kk][...]
n = self.parameters['nx']
if self.dns_type in ['filtered_slices',
'filtered_acceleration']:
@@ -799,9 +799,9 @@ class PP(_code):
if 'field_dtype' in df.keys():
# we don't need to do anything, raw binary files are used
return None
- last_iteration = df['iteration'].value
- cppf = df['parameters/checkpoints_per_file'].value
- niter_out = df['parameters/niter_out'].value
+ last_iteration = df['iteration'][...]
+ cppf = df['parameters/checkpoints_per_file'][...]
+ niter_out = df['parameters/niter_out'][...]
with h5py.File(os.path.join(self.work_dir, self.simname + '_fields.h5'), 'a') as ff:
ff.require_group('vorticity')
ff.require_group('vorticity/complex')
diff --git a/bfps/_base.py b/bfps/_base.py
index 3d7c747b..086adea3 100644
--- a/bfps/_base.py
+++ b/bfps/_base.py
@@ -231,9 +231,9 @@ class _base(object):
for k in data_file['parameters'].keys():
if k in self.parameters.keys():
if type(self.parameters[k]) in [int, str, float]:
- self.parameters[k] = type(self.parameters[k])(data_file['parameters/' + k].value)
+ self.parameters[k] = type(self.parameters[k])(data_file['parameters/' + k][...])
else:
- self.parameters[k] = data_file['parameters/' + k].value
+ self.parameters[k] = data_file['parameters/' + k][...]
return None
def pars_from_namespace(
self,
diff --git a/bfps/_code.py b/bfps/_code.py
index f997d651..d791be61 100644
--- a/bfps/_code.py
+++ b/bfps/_code.py
@@ -245,7 +245,7 @@ class _code(_base):
no_debug = False):
self.read_parameters()
with h5py.File(os.path.join(self.work_dir, self.simname + '.h5'), 'r') as data_file:
- iter0 = data_file['iteration'].value
+ iter0 = data_file['iteration'][...]
if not os.path.isdir(self.work_dir):
os.makedirs(self.work_dir)
if not os.path.exists(os.path.join(self.work_dir, self.name)):
diff --git a/bfps/test/test_bfps_NSVEparticles.py b/bfps/test/test_bfps_NSVEparticles.py
index fe1e7875..e9abe672 100644
--- a/bfps/test/test_bfps_NSVEparticles.py
+++ b/bfps/test/test_bfps_NSVEparticles.py
@@ -66,14 +66,14 @@ def main():
'r')
f1 = h5py.File(c.get_checkpoint_0_fname(), 'r')
for iteration in [0, 32, 64]:
- field0 = f0['vorticity/complex/{0}'.format(iteration)].value
- field1 = f1['vorticity/complex/{0}'.format(iteration)].value
+ field0 = f0['vorticity/complex/{0}'.format(iteration)][...]
+ field1 = f1['vorticity/complex/{0}'.format(iteration)][...]
field_error = np.max(np.abs(field0 - field1))
- x0 = f0['tracers0/state/{0}'.format(iteration)].value
- x1 = f1['tracers0/state/{0}'.format(iteration)].value
+ x0 = f0['tracers0/state/{0}'.format(iteration)][...]
+ x1 = f1['tracers0/state/{0}'.format(iteration)][...]
traj_error = np.max(np.abs(x0 - x1))
- y0 = f0['tracers0/rhs/{0}'.format(iteration)].value
- y1 = f1['tracers0/rhs/{0}'.format(iteration)].value
+ y0 = f0['tracers0/rhs/{0}'.format(iteration)][...]
+ y1 = f1['tracers0/rhs/{0}'.format(iteration)][...]
rhs_error = np.max(np.abs(y0 - y1))
assert(field_error < 1e-5)
assert(traj_error < 1e-5)
diff --git a/bfps/test/test_bfps_resize.py b/bfps/test/test_bfps_resize.py
index ce0a051d..2dfb4c69 100644
--- a/bfps/test/test_bfps_resize.py
+++ b/bfps/test/test_bfps_resize.py
@@ -46,8 +46,8 @@ def main():
sys.argv[1:])
f0 = h5py.File(c.get_checkpoint_0_fname(), 'r')
f1 = h5py.File('pp_resize_test_fields.h5', 'r')
- d0 = f0['vorticity/complex/0'].value
- d1 = f1['vorticity/complex/0'].value
+ d0 = f0['vorticity/complex/0'][...]
+ d1 = f1['vorticity/complex/0'][...]
small_kdata = pyfftw.n_byte_align_empty(
(32, 32, 17, 3),
pyfftw.simd_alignment,
diff --git a/bfps/test/test_fftw.py b/bfps/test/test_fftw.py
index 3de2d97d..f129d57e 100644
--- a/bfps/test/test_fftw.py
+++ b/bfps/test/test_fftw.py
@@ -32,8 +32,8 @@ def main():
sys.argv[1:])
df = h5py.File(c.simname + '.h5', 'r')
df = h5py.File(c.simname + '_fields.h5', 'r')
- field1_complex = df['field1/complex/0'].value
- field1_real = df['field1/real/0'].value
+ field1_complex = df['field1/complex/0'][...]
+ field1_real = df['field1/real/0'][...]
npoints = field1_real.size//3
np_field1_real = np.fft.irfftn(field1_complex, axes = (0, 1, 2)).transpose(1, 0, 2, 3)
diff --git a/bfps/test/test_interpolation.py b/bfps/test/test_interpolation.py
index eeb40248..a4fea59f 100644
--- a/bfps/test/test_interpolation.py
+++ b/bfps/test/test_interpolation.py
@@ -32,11 +32,11 @@ def main():
ofile = h5py.File(
'test_output.h5',
'r')
- pos0 = ifile['tracers0/state/0'].value
- pos1 = ofile['tracers0/position/0'].value
+ pos0 = ifile['tracers0/state/0'][...]
+ pos1 = ofile['tracers0/position/0'][...]
assert(np.max(np.abs(pos0-pos1) / np.abs(pos0)) <= 1e-5)
- vort0 = ofile['tracers0/vorticity/0'].value
- vel_gradient = ofile['tracers0/velocity_gradient/0'].value
+ vort0 = ofile['tracers0/vorticity/0'][...]
+ vel_gradient = ofile['tracers0/velocity_gradient/0'][...]
vort1 = vort0.copy()
vort1[:, 0] = vel_gradient[:, 5] - vel_gradient[:, 7]
vort1[:, 1] = vel_gradient[:, 6] - vel_gradient[:, 2]
diff --git a/bfps/test/test_particle_clouds.py b/bfps/test/test_particle_clouds.py
index 5d204539..aef70598 100644
--- a/bfps/test/test_particle_clouds.py
+++ b/bfps/test/test_particle_clouds.py
@@ -47,8 +47,8 @@ def main():
del c.parameters['nparticles']
del c.parameters['tracers1_integration_steps']
ic_file = h5py.File(c.get_checkpoint_0_fname(), 'a')
- ic_file['tracers0/state/0'] = ic_file['tracers1/state/0'].value.reshape(nclouds, nparticles_per_cloud, 3)
- ic_file['tracers0/rhs/0'] = ic_file['tracers1/rhs/0'].value.reshape(4, nclouds, nparticles_per_cloud, 3)
+ ic_file['tracers0/state/0'] = ic_file['tracers1/state/0'][...].reshape(nclouds, nparticles_per_cloud, 3)
+ ic_file['tracers0/rhs/0'] = ic_file['tracers1/rhs/0'][...].reshape(4, nclouds, nparticles_per_cloud, 3)
ic_file.close()
c.launch(
['NSVEparticles',
@@ -73,14 +73,14 @@ def main():
'r')
f1 = h5py.File(c.get_checkpoint_0_fname(), 'r')
for iteration in [0, 32, 64]:
- field0 = f0['vorticity/complex/{0}'.format(iteration)].value
- field1 = f1['vorticity/complex/{0}'.format(iteration)].value
+ field0 = f0['vorticity/complex/{0}'.format(iteration)][...]
+ field1 = f1['vorticity/complex/{0}'.format(iteration)][...]
field_error = np.max(np.abs(field0 - field1))
- x0 = f0['tracers0/state/{0}'.format(iteration)].value
- x1 = f1['tracers0/state/{0}'.format(iteration)].value.reshape(x0.shape)
+ x0 = f0['tracers0/state/{0}'.format(iteration)][...]
+ x1 = f1['tracers0/state/{0}'.format(iteration)][...].reshape(x0.shape)
traj_error = np.max(np.abs(x0 - x1))
- y0 = f0['tracers0/rhs/{0}'.format(iteration)].value
- y1 = f1['tracers0/rhs/{0}'.format(iteration)].value.reshape(y0.shape)
+ y0 = f0['tracers0/rhs/{0}'.format(iteration)][...]
+ y1 = f1['tracers0/rhs/{0}'.format(iteration)][...].reshape(y0.shape)
rhs_error = np.max(np.abs(y0 - y1))
assert(field_error < 1e-5)
assert(traj_error < 1e-5)
diff --git a/bfps/test/test_particles.py b/bfps/test/test_particles.py
index 6d3abec1..c3249a98 100644
--- a/bfps/test/test_particles.py
+++ b/bfps/test/test_particles.py
@@ -68,7 +68,7 @@ def main():
f = plt.figure()
a = f.add_subplot(111)
for iteration in range(0, niterations*njobs+1, niterations//2):
- x = pf['tracers0/position/{0}'.format(iteration)].value
+ x = pf['tracers0/position/{0}'.format(iteration)][...]
hist, bins = np.histogram(
np.sum(x**2, axis = -1).flatten()**.5,
bins = 40)
@@ -83,7 +83,7 @@ def main():
f = plt.figure()
a = f.add_subplot(111)
for iteration in range(0, niterations*njobs+1, niterations//2):
- x = pf['tracers0/orientation/{0}'.format(iteration)].value
+ x = pf['tracers0/orientation/{0}'.format(iteration)][...]
hist, bins = np.histogram(
np.sum(x**2, axis = -1).flatten()**.5,
bins = np.linspace(0, 2, 40))
@@ -96,14 +96,14 @@ def main():
plt.close(f)
# compared sampled positions with checkpoint positions
for iteration in range(0, niterations*njobs+1, niterations):
- x = pf['tracers0/position/{0}'.format(iteration)].value
- s = cf['tracers0/state/{0}'.format(iteration)].value
+ x = pf['tracers0/position/{0}'.format(iteration)][...]
+ s = cf['tracers0/state/{0}'.format(iteration)][...]
distance = (np.max(np.abs(x - s[..., :3]) /
np.maximum(np.ones(x.shape),
np.maximum(np.abs(x),
np.abs(s[..., :3])))))
assert(distance < 1e-14)
- x = pf['tracers0/orientation/{0}'.format(iteration)].value
+ x = pf['tracers0/orientation/{0}'.format(iteration)][...]
distance = (np.max(np.abs(x - s[..., 3:]) /
np.maximum(np.ones(x.shape),
np.maximum(np.abs(x),
@@ -115,7 +115,7 @@ def main():
f = plt.figure()
a = f.add_subplot(111)
for iteration in range(0, niterations*njobs+1, niterations//4):
- x = pf['tracers0/orientation/{0}'.format(iteration)].value
+ x = pf['tracers0/orientation/{0}'.format(iteration)][...]
hist, bins = np.histogram(
x.flatten(),
bins = 100)
diff --git a/bfps/tools.py b/bfps/tools.py
index a3fbc9d9..9acf4e22 100644
--- a/bfps/tools.py
+++ b/bfps/tools.py
@@ -284,10 +284,10 @@ def particle_finite_diff_test(
pf = c.get_particle_file()
group = pf['tracers{0}'.format(species)]
acc_on = 'acceleration' in group.keys()
- pos = group['state'].value
- vel = group['velocity'].value
+ pos = group['state'][...]
+ vel = group['velocity'][...]
if acc_on:
- acc = group['acceleration'].value
+ acc = group['acceleration'][...]
n = m
fc = get_fornberg_coeffs(0, range(-n, n+1))
dt = c.parameters['dt']*c.parameters['niter_part']
@@ -311,7 +311,7 @@ def particle_finite_diff_test(
if interp_name not in pars.keys():
# old format
interp_name = 'tracers{0}_field'.format(species)
- interp_name = pars[interp_name].value
+ interp_name = pars[interp_name][...]
if type(interp_name) == bytes:
if sys.version_info[0] == 3:
interp_name = str(interp_name, 'ASCII')
@@ -319,11 +319,11 @@ def particle_finite_diff_test(
interp_name = str(interp_name)
to_print = (
'steps={0}, interp={1}, neighbours={2}, '.format(
- pars['tracers{0}_integration_steps'.format(species)].value,
- pars[interp_name + '_type'].value,
- pars[interp_name + '_neighbours'].value))
+ pars['tracers{0}_integration_steps'.format(species)][...],
+ pars[interp_name + '_type'][...],
+ pars[interp_name + '_neighbours'][...]))
if 'spline' in interp_name:
- to_print += 'smoothness = {0}, '.format(pars[interp_name + '_smoothness'].value)
+ to_print += 'smoothness = {0}, '.format(pars[interp_name + '_smoothness'][...])
to_print += (
'SNR d1p-vel={0:.3f}'.format(np.mean(snr_vel1)))
if acc_on:
diff --git a/tests/test_field_class.py b/tests/test_field_class.py
index 110d9be6..ef0cc851 100644
--- a/tests/test_field_class.py
+++ b/tests/test_field_class.py
@@ -142,9 +142,9 @@ def main():
'--ncpu', '2'])
f = h5py.File('field.h5', 'r')
- #err0 = np.max(np.abs(f['scal_tmp/real/0'].value - rdata)) / np.mean(np.abs(rdata))
- #err1 = np.max(np.abs(f['scal/real/0'].value/(n**3) - rdata)) / np.mean(np.abs(rdata))
- #err2 = np.max(np.abs(f['scal_tmp/complex/0'].value/(n**3) - cdata)) / np.mean(np.abs(cdata))
+ #err0 = np.max(np.abs(f['scal_tmp/real/0'][...] - rdata)) / np.mean(np.abs(rdata))
+ #err1 = np.max(np.abs(f['scal/real/0'][...]/(n**3) - rdata)) / np.mean(np.abs(rdata))
+ #err2 = np.max(np.abs(f['scal_tmp/complex/0'][...]/(n**3) - cdata)) / np.mean(np.abs(cdata))
#print(err0, err1, err2)
#assert(err0 < 1e-5)
#assert(err1 < 1e-5)
diff --git a/tests/test_filters.py b/tests/test_filters.py
index b6e2aedb..b3c24bf7 100644
--- a/tests/test_filters.py
+++ b/tests/test_filters.py
@@ -80,9 +80,9 @@ def filter_comparison(
dd = None,
base_name = 'filter_test_',
dim = 0):
- b = dd.df['ball/real/{0}'.format(dim)].value
- g = dd.df['Gauss/real/{0}'.format(dim)].value
- s = dd.df['sharp_Fourier_sphere/real/{0}'.format(dim)].value
+ b = dd.df['ball/real/{0}'.format(dim)][...]
+ g = dd.df['Gauss/real/{0}'.format(dim)][...]
+ s = dd.df['sharp_Fourier_sphere/real/{0}'.format(dim)][...]
d3V = dd.grid_spacing['x']*dd.grid_spacing['y']*dd.grid_spacing['z']
print(np.sum(b)*d3V)
print(np.sum(g)*d3V)
@@ -164,7 +164,7 @@ def resolution_comparison(
f = plt.figure(figsize = (6, 5))
a = f.add_subplot(111)
for dd in dlist:
- s0 = dd.df[filter_type + '/real/{0}'.format(dim)].value
+ s0 = dd.df[filter_type + '/real/{0}'.format(dim)][...]
a.plot(dd.get_coordinate('z'),
s0[:, 0, 0],
label = '{0}'.format(dd.simname))
@@ -182,7 +182,7 @@ class sim_data:
pfile = h5py.File(simname + '.h5', 'r')
self.parameters = {}
for kk in pfile['parameters'].keys():
- self.parameters[kk] = pfile['parameters/' + kk].value
+ self.parameters[kk] = pfile['parameters/' + kk][...]
self.grid_spacing = {}
for kk in ['x', 'y', 'z']:
self.grid_spacing[kk] = 2*np.pi / (self.parameters['dk' + kk] * self.parameters['n' + kk])
diff --git a/tests/test_particles.py b/tests/test_particles.py
index 7c7c8661..6be07642 100644
--- a/tests/test_particles.py
+++ b/tests/test_particles.py
@@ -118,7 +118,7 @@ class err_finder:
for c in self.clist]
self.ctraj = [None]
for i in range(1, self.clist[0].particle_species):
- self.ctraj.append([self.clist[j].get_particle_file()['tracers{0}/state'.format(i)].value.transpose((0, 2, 1))
+ self.ctraj.append([self.clist[j].get_particle_file()['tracers{0}/state'.format(i)][...].transpose((0, 2, 1))
for j in range(len(self.clist))])
return None
def get_AB_err(self, nsubsteps = 1):
@@ -178,7 +178,7 @@ if __name__ == '__main__':
a = fig.add_subplot(111)
for s in range(1, 5):
ef.get_AB_err(s)
- errlist = [np.average(np.abs(ef.clist[i].get_particle_file()['tracers{0}/state'.format(s)].value[-1, :, :3] - ef.xAB[i][-1].T))
+ errlist = [np.average(np.abs(ef.clist[i].get_particle_file()['tracers{0}/state'.format(s)][...][-1, :, :3] - ef.xAB[i][-1].T))
for i in range(len(ef.clist))]
a.plot(ef.dtlist, errlist,
label = 'directAB{0}'.format(s),
--
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