PYTHON: Implement AmunH5 class for Amun's HDF5 format.
Mark the previous subroutines deprecated. Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
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@ -33,12 +33,117 @@
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--------------------------------------------------------------------------------
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"""
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from .interpolation import interpolate
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import h5py as h5
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import numpy as np
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import os.path as op
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import sys
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from .amun import Amun
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class AmunH5(Amun):
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"""AMUN H5 snapshot class"""
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def __init_snapshot__(self):
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"""
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Initializes the snapshots by verifying if the file is indeed
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in the AmunH5 format.
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"""
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import h5py
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if not self.path_is_file:
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raise Exception("AmunH5 requires a file not directory as the argument!")
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with h5py.File(self.path, 'r') as h5:
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if 'codes' in h5.attrs:
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if h5.attrs['code'].astype(str) == "AMUN":
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self.dataformat = 'AmunH5'
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else:
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raise Exception("'{}' contains attribute 'code', but its content is not 'AMUN'!".format(self.path))
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elif 'attributes' in h5 and 'coordinates' in h5 and 'variables' in h5:
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self.dataformat = 'AmunH5'
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else:
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raise Exception("{} misses one of these groups: 'attributes', 'coordinates' or 'variables'!".format(self.path))
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def __fill_attributes__(self):
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"""
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Read attributes from the snapshot file and fill up
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the corresponding attribute dictionary.
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"""
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import h5py
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exclude_list = ['nseeds', 'seeds', 'dblocks', 'nproc', 'dims', 'dtn', 'last_id', 'mblocks']
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with h5py.File(self.path, 'r') as h5:
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for aname in h5['attributes'].attrs:
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if not aname in exclude_list:
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attr = h5['attributes'].attrs[aname]
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if attr.dtype == 'float64' or attr.dtype == 'float32' or \
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attr.dtype == 'int64' or attr.dtype == 'int32':
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if len(attr) > 1:
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self.attributes[aname] = attr.tolist()
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else:
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self.attributes[aname] = attr[0]
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else:
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self.attributes[aname] = attr[0].astype(str)
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if not 'nchunks' in self.attributes and 'nprocs' in self.attributes:
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self.attributes['nchunks'] = self.attributes['nprocs']
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del self.attributes['nprocs']
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if 'rdims' in self.attributes:
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self.attributes['xblocks'] = self.attributes['rdims'][0]
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self.attributes['yblocks'] = self.attributes['rdims'][1]
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if self.attributes['ndims'] == 3:
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self.attributes['zblocks'] = self.attributes['rdims'][2]
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del self.attributes['rdims']
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def __fill_variables__(self):
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"""
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Read variable names from the snapshot file and fill up
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the corresponding variable list.
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"""
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import h5py
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with h5py.File(self.path, 'r') as h5:
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for variable in h5['variables']:
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v = variable.strip()
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self.variables[v] = v
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def __fill_chunks__(self):
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"""
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Retrieve metadata about datablocks stored in the snapshot's chunks.
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"""
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import h5py, numpy, os
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self.chunkname = 'p{:06d}'.format(self.attributes['isnap']) + '_{:05d}.h5'
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for n in range(self.attributes['nchunks']):
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self.chunks[n] = dict()
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self.chunks[n]['filename'] = self.chunkname.format(n)
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cname = os.path.join(self.dirname, self.chunks[n]['filename'])
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if os.path.exists(cname):
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with h5py.File(cname, 'r') as h5:
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self.chunks[n]['dblocks'] = h5['attributes'].attrs['dblocks'][0]
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self.chunks[n]['levels'] = numpy.array(h5['coordinates']['levels'])
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self.chunks[n]['bounds'] = numpy.array(h5['coordinates']['bounds'])
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self.chunks[n]['coords'] = numpy.array(h5['coordinates']['coords'])
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else:
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raise Exception("Snapshot's chunk '{}' not present!".format(cname))
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def __read_binary_data__(self, dataset_name, chunk_number):
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"""
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Gets the dataset array from a given snapshot's chunk.
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"""
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import h5py, numpy, os
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cname = os.path.join(self.dirname, self.chunks[chunk_number]['filename'])
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with h5py.File(cname, 'r') as h5:
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return numpy.array(h5['variables'][dataset_name])
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#===============================================================================
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'''
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DEPRECATED FUNCTIONS
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'''
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def amun_compatible(fname):
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'''
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@ -57,6 +162,11 @@ def amun_compatible(fname):
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comp = amun_compatible('p000010_00000.h5')
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'''
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from warnings import warn
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import h5py as h5
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warn('This function is deprecated', DeprecationWarning, stacklevel=2)
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with h5.File(fname, 'r') as f:
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if 'codes' in f.attrs:
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if f.attrs['code'].astype(str) == "AMUN":
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@ -92,6 +202,12 @@ def amun_attribute(fname, aname):
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time = amun_attribute('p000010_00000.h5', 'time')
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'''
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from warnings import warn
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import h5py as h5
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import numpy as np
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warn('This function is deprecated', DeprecationWarning, stacklevel=2)
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if not amun_compatible(fname):
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return None
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@ -126,6 +242,12 @@ def amun_coordinate(fname, iname):
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bounds = amun_coordinate('p000010_00000.h5', 'bounds')
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'''
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from warnings import warn
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import h5py as h5
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import numpy as np
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warn('This function is deprecated', DeprecationWarning, stacklevel=2)
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if not amun_compatible(fname):
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return None
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@ -158,10 +280,18 @@ def amun_dataset(fname, vname, shrink=1, interpolation='rebin', order=3, progres
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dn = amun_dataset('p000010_00000.h5', 'dens')
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'''
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from .interpolation import interpolate
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from warnings import warn
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import h5py as h5
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import numpy as np
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import os, sys
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warn('This function is deprecated', DeprecationWarning, stacklevel=2)
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if not amun_compatible(fname):
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return None
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dname = op.dirname(fname)
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dname = os.path.dirname(fname)
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if progress:
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sys.stdout.write("Data file path:\n '%s'\n" % (dname))
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@ -265,7 +395,7 @@ def amun_dataset(fname, vname, shrink=1, interpolation='rebin', order=3, progres
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levs = []
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for n in range(nc):
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fname = 'p%06d_%05d.h5' % (nr, n)
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lname = op.join(dname, fname)
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lname = os.path.join(dname, fname)
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dblocks = amun_attribute(lname, 'dblocks')
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if dblocks > 0:
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levs = np.append(levs, [amun_coordinate(lname, 'levels')])
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@ -282,7 +412,7 @@ def amun_dataset(fname, vname, shrink=1, interpolation='rebin', order=3, progres
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nb = 0
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for n in range(nc):
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fname = 'p%06d_%05d.h5' % (nr, n)
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lname = op.join(dname, fname)
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lname = os.path.join(dname, fname)
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dblocks = amun_attribute(lname, 'dblocks')
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if dblocks > 0:
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levels = amun_coordinate(lname, 'levels')
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@ -475,7 +605,11 @@ def amun_dataset_vtk(fname, vname, label=None, compression=None, compression_lev
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'''
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from .octree import OcBase, OcNode
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from .vtkio import WriteVTK
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import os
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from warnings import warn
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import numpy as np
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import os, sys
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warn('This function is deprecated', DeprecationWarning, stacklevel=2)
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if not amun_compatible(fname):
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return None
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@ -487,7 +621,7 @@ def amun_dataset_vtk(fname, vname, label=None, compression=None, compression_lev
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if label == None:
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label = vname
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dname = op.dirname(fname)
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dname = os.path.dirname(fname)
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if progress:
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sys.stdout.write("Data file path:\n '%s'\n" % (dname))
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@ -583,7 +717,7 @@ def amun_dataset_vtk(fname, vname, label=None, compression=None, compression_lev
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levs = []
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for n in range(nc):
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fname = 'p%06d_%05d.h5' % (nr, n)
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lname = op.join(dname, fname)
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lname = os.path.join(dname, fname)
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dblocks = amun_attribute(lname, 'dblocks')
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if dblocks > 0:
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levs = np.append(levs, [amun_coordinate(lname, 'levels')])
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@ -597,7 +731,7 @@ def amun_dataset_vtk(fname, vname, label=None, compression=None, compression_lev
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nb = 0
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for n in range(nc):
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fname = 'p%06d_%05d.h5' % (nr, n)
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lname = op.join(dname, fname)
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lname = os.path.join(dname, fname)
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dblocks = amun_attribute(lname, 'dblocks')
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if dblocks > 0:
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levels = amun_coordinate(lname, 'levels')
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@ -767,7 +901,7 @@ def amun_dataset_vtk(fname, vname, label=None, compression=None, compression_lev
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ofile = "{}_{:06d}.vthb".format(vname, nr)
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opath = "{}_{:06d}".format(vname, nr)
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if not op.exists(opath):
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if not os.path.exists(opath):
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os.makedirs(opath)
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with open(ofile, 'w') as vtk:
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vtk.write('<VTKFile type="vtkOverlappingAMR" version="1.1" ' + \
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@ -791,7 +925,7 @@ def amun_dataset_vtk(fname, vname, label=None, compression=None, compression_lev
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up = lo + bm - 1
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ll = np.stack((lo,up)).T.flatten()
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if item.hasData:
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vfile = op.join(opath, fmt.format(vname, lv, no))
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vfile = os.path.join(opath, fmt.format(vname, lv, no))
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WriteVTK(vfile, label, item.data, \
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origin = (item.lower[0], item.lower[1], item.lower[2]), \
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spacing = (cw[0], cw[1], cw[2]), \
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