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Merge branch 'master' into reconnection

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This commit is contained in:
Grzegorz Kowal 2021-10-06 18:08:55 -03:00
commit 6c7aa6dd13
5 changed files with 19 additions and 11 deletions
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2
python/amunpy/setup.py
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@ -5,7 +5,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setuptools.setup(
name="amunpy",
version="0.9.4",
version="0.9.5",
author="Grzegorz Kowal",
author_email="grzegorz@amuncode.org",
description="Python Interface for the AMUN code's snapshots",

2
python/amunpy/src/amunpy/__init__.py
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@ -21,6 +21,6 @@ __all__ = [ 'AmunXML', 'AmunH5', 'WriteVTK', \
__author__ = "Grzegorz Kowal"
__copyright__ = "Copyright 2018-2021, Grzegorz Kowal <grzegorz@amuncode.org>"
__version__ = "0.9.4"
__version__ = "0.9.5"
__maintainer__ = "Grzegorz Kowal"
__email__ = "grzegorz@amuncode.org"

2
python/amunpy/src/amunpy/amun.py
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@ -140,7 +140,7 @@ class Amun:
Add additional attributes.
"""
if not 'toplev' in self.attributes:
self.attributes['toplev'] = max([self.chunks[n]['levels'].max() for n in range(self.attributes['nchunks'])])
self.attributes['toplev'] = max([max(chunk['levels']) if chunk['dblocks'] > 0 else 1 for chunk in self.chunks.values()])
if not 'xlen' in self.attributes:
self.attributes['xlen'] = self.attributes['xmax'] - self.attributes['xmin']

18
python/amunpy/src/amunpy/amunh5.py
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@ -117,10 +117,14 @@ class AmunH5(Amun):
if os.path.exists(cname):
with h5py.File(cname, 'r') as h5:
self.chunks[n]['dblocks'] = h5['attributes'].attrs['dblocks'][0]
self.chunks[n]['levels'] = numpy.array(h5['coordinates']['levels'])
self.chunks[n]['bounds'] = numpy.array(h5['coordinates']['bounds'])
self.chunks[n]['coords'] = numpy.array(h5['coordinates']['coords'])
if self.chunks[n]['dblocks'] > 0:
self.chunks[n]['levels'] = numpy.array(h5['coordinates']['levels'])
self.chunks[n]['bounds'] = numpy.array(h5['coordinates']['bounds'])
self.chunks[n]['coords'] = numpy.array(h5['coordinates']['coords'])
else:
self.chunks[n]['levels'] = None
self.chunks[n]['coords'] = None
self.chunks[n]['bounds'] = None
else:
raise Exception("Snapshot's chunk '{}' not present!".format(cname))
@ -133,4 +137,8 @@ class AmunH5(Amun):
cname = os.path.join(self.dirname, self.chunks[chunk_number]['filename'])
with h5py.File(cname, 'r') as h5:
return numpy.array(h5['variables'][dataset_name])
dset = numpy.array(h5['variables'][dataset_name])
if self.attributes['ndims'] == 3:
return dset
else:
return dset[0,:,:,:]

6
python/amunpy/src/amunpy/amunxml.py
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@ -168,9 +168,9 @@ class AmunXML(Amun):
self.chunks[n]['bounds'] = numpy.array([bounds[:,:,ii[p]].T for p in range(self.chunks[n]['dblocks'])]).T
else:
self.chunks[n]['levels'] = numpy.zeros((1), dtype = numpy.int32)
self.chunks[n]['coords'] = numpy.zeros((3,1), dtype = numpy.int32)
self.chunks[n]['bounds'] = numpy.zeros((2,3,1), dtype = numpy.float64)
self.chunks[n]['levels'] = None
self.chunks[n]['coords'] = None
self.chunks[n]['bounds'] = None
def __read_binary_data__(self, dataset_name, chunk_number):