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Allows hdf5_restore to restore from any save
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- Includes detection and restoration of saves written by UETOOLS
- Makes some modifications to the user prompts during read
  - Specifies the file structure detected
  - Specifies the file read by name
  - Explicitly reports success
- Changes most of the structure of the restore
- No impact on usage
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@holm10
holm10 committed Jan 10, 2024
1 parent fb4896f commit 2ff7a5b
Showing 1 changed file with 57 additions and 78 deletions.
135 changes: 57 additions & 78 deletions pyscripts/hdf5.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
import numpy as np
import h5py
import uedge
try:
Expand All @@ -19,81 +18,60 @@ def hdf5_restore(file):
and will attempt to restore all datasets. This will restore a file saved by either
hdf5_save or hdf5_dump.
"""
try:
hf = h5py.File(file, 'r')
except:
print("Couldn't open hdf5 file ", file)
raise
from os.path import exists
from numpy import array
from h5py import File

try:
dummy = hf['bbb'] # force an exception if the group not there
hfb = hf.get('bbb')
try:
for var in ['tes', 'tis', 'ups', 'nis', 'phis', 'ngs', 'tgs']:
packageobject('bbb').__setattr__(var, hf['bbb'][var][()])
except:
raise
# Check that the requested file exists
if not exists(file):
raise Exception("{} not found: Aborting!".format(file))

except:
print("Old style hdf5 file")
try:
bbb.ngs[...] = np.array(hf.get('ngs@bbb'))
except ValueError as error:
print("Couldn't read ngs from ", file)
print(error)
except:
print("Couldn't read ngs from ", file)
try:
bbb.nis[...] = np.array(hf.get('nis@bbb'))
except ValueError as error:
print("Couldn't read nis from ", file)
print(error)
except:
print("Couldn't read nis from ", file)
try:
bbb.phis[...] = np.array(hf.get('phis@bbb'))
except ValueError as error:
print("Couldn't read phis from ", file)
print(error)
except:
print("Couldn't read phis from ", file)
try:
bbb.tes[...] = np.array(hf.get('tes@bbb'))
except ValueError as error:
print("Couldn't read tes from ", file)
print(error)
except:
print("Couldn't read tes from ", file)
try:
bbb.tis[...] = np.array(hf.get('tis@bbb'))
except ValueError as error:
print("Couldn't read tis from ", file)
print(error)
except:
print("Couldn't read tis from ", file)
try:
bbb.ups[...] = np.array(hf.get('ups@bbb'))
except ValueError as error:
print("Couldn't read ups from ", file)
print(error)
except:
print("Couldn't read ups from ", file)
try:
bbb.tgs[...] = np.array(hf.get('tgs@bbb'))
except ValueError as error:
print("Couldn't read tgs from ", file)
print(error)
except:
print("Couldn't read tgs from ", file)
try:
bbb.tipers[...] = np.array(hf.get('tipers@bbb'))
except ValueError as error:
print("Couldn't read tipers from ", file)
print(error)
except:
print("Couldn't read tipers from ", file)
# The standard restore variables
varlist = ['tes', 'tis', 'ups', 'nis', 'phis', 'ngs']
# Newer versions of UEDGE introduce additional, newer variables,
# which are to be restored if available:
# - tgs: gaseous temperture for solving gaseous energy eqs
# - tipers: perpendicular ion temperature
for newvar in ['tgs', 'tipers']:
# Ensure any available new variables also are restored
if newvar in packageobject("bbb").varlist():
varlist.append(newvar)

hf.close()
with File(file, "r") as hf:
# Check whether an (very) old version of the save file is used
if "nis@bbb" in list(hf.keys()):
print("\nReading old style, flat-structured, save-file '{}'.".format(file))
for var in varlist:
# Restore variable if available from save
try:
packageobject('bbb').__setattr__(
var,
array(hf.get('{}@bbb'.format(var)))
)
except ValueError as error:
print("Couldn't read {} from {}".format(var, file))
print(error)
except:
print("Couldn't read {} from {}".format(var, file))
return True
# Check whether file is UETOOLS-style file
if "restore" in list(hf.keys()):
print("\nReading UETOOLS style save-file '{}'.".format(file))
restoregroup = hf['restore/bbb']
# Check whether file is uedge.hdf5-style file
elif "bbb" in list(hf.keys()):
print("\nReading uedge.hdf5-style save-file '{}'.".format(file))
restoregroup = hf['bbb']
# Unknown file structure, abort
else:
raise Exception("\nUnable to read data from {}".file(file))
# Read all the required restore variables
for var in varlist:
try:
packageobject('bbb').__setattr__(var, restoregroup[var][()])
except:
raise
print(">>> Save read successfully")
return True


Expand Down Expand Up @@ -279,6 +257,7 @@ def hdf5_restore_dump(file, scope=None, hdffile=None,quiet=False):
This is called by hdf5_restore and the recommended way
to restore.
"""
from numpy import char, array
if hdffile == None:
try:
hf = h5py.File(file, 'r')
Expand All @@ -295,9 +274,9 @@ def hdf5_restore_dump(file, scope=None, hdffile=None,quiet=False):
print('File attributes:')
print(' written on: ', g.attrs['ctime'])
print(' by code: ', g.attrs['code'])
print(' version: ', np.char.strip(g.attrs['ver']))
print(' physics tag: ', np.char.strip(g.attrs['ver']))
print(' python version: ', np.char.strip(g.attrs['pyver']))
print(' version: ', char.strip(g.attrs['ver']))
print(' physics tag: ', char.strip(g.attrs['ver']))
print(' python version: ', char.strip(g.attrs['pyver']))
except:
if not quiet:
print('No file attributes, trying to restore')
Expand All @@ -307,7 +286,7 @@ def hdf5_restore_dump(file, scope=None, hdffile=None,quiet=False):
if vt[1] == 'globals':
if scope != None:
if dset.size > 1:
scope[vt[2]] = np.array(dset[()])
scope[vt[2]] = array(dset[()])
else:
scope[vt[2]] = dset[()]

Expand All @@ -316,7 +295,7 @@ def hdf5_restore_dump(file, scope=None, hdffile=None,quiet=False):
pck = packagename2object(vt[1])
po = pck.getpyobject(vt[2])
if dset.size > 1:
po[...] = np.array(dset[()])
po[...] = array(dset[()])
else:
setattr(pck, vt[2], dset[()])
except ValueError as error:
Expand Down

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