def to_file(obj, fname, fmt=None, overwrite=True, warn=True, **kwargs):
"""Dispatch correct file writer based on fmt (if specified) or guess
based on file name's extension"""
if fmt is None:
rootname, ext = os.path.splitext(fname)
ext = ext.replace('.', '').lower()
else:
rootname = fname
ext = fmt.lower()
if ext in ZIP_EXTS or ext in XOR_EXTS:
rootname, inner_ext = os.path.splitext(rootname)
inner_ext = inner_ext.replace('.', '').lower()
ext = inner_ext
if ext in jsons.JSON_EXTS:
return jsons.to_json(obj,
fname,
overwrite=overwrite,
warn=warn,
**kwargs)
elif ext in hdf.HDF5_EXTS:
return hdf.to_hdf(obj, fname, overwrite=overwrite, warn=warn, **kwargs)
elif ext in PKL_EXTS:
return to_pickle(obj, fname, overwrite=overwrite, warn=warn, **kwargs)
elif ext in TXT_EXTS:
if kwargs:
raise ValueError('Following additional keyword arguments not'
' accepted when writing to text file: %s' %
kwargs.keys())
return to_txt(obj, fname)
else:
errmsg = 'Unrecognized file type/extension: ' + ext
log.logging.error(errmsg)
raise TypeError(errmsg)
def to_file(obj, fname, fmt=None):
"""Dispatch correct file writer based on fmt (if specified) or guess
based on file name's extension"""
if fmt is None:
base, ext = os.path.splitext(fname)
ext = ext.replace('.', '').lower()
else:
ext = fmt.lower()
if ext in JSON_EXTS:
return jsons.to_json(obj, fname)
elif ext in HDF5_EXTS:
return hdf.to_hdf(obj, fname)
elif ext in PKL_EXTS:
return cPickle.dump(obj, file(fname, 'wb'))
else:
errmsg = 'Unrecognized file type/extension: ' + ext
logging.error(errmsg)
raise TypeError(errmsg)
def to_file(obj, fname, fmt=None):
"""Dispatch correct file writer based on fmt (if specified) or guess
based on file name's extension"""
if fmt is None:
base, ext = os.path.splitext(fname)
ext = ext.replace('.', '').lower()
else:
ext = fmt.lower()
if ext in JSON_EXTS:
return jsons.to_json(obj, fname)
elif ext in HDF5_EXTS:
return hdf.to_hdf(obj, fname)
elif ext in PKL_EXTS:
return cPickle.dump(obj, file(fname, 'wb'))
else:
errmsg = 'Unrecognized file type/extension: ' + ext
logging.error(errmsg)
raise TypeError(errmsg)
def save(self, fname, **kwargs):
hdf.to_hdf(self, fname, attrs=self.metadata, **kwargs)
def store_kernels(self, filename, fmt='hdf5'):
"""Store reconstruction kernels in HDF5 format"""
if fmt.lower() in ['hdf', 'h5', 'hdf5']:
hdf.to_hdf(self.kernels, filename)
else:
raise NotImplementedError('Only hdf5 is implemented')
print "Skipping file: ", filename
continue
if not minimizer_settings:
minimizer_settings = data['minimizer_settings']
if not template_settings:
template_settings = data['template_settings']
if not pseudo_data_settings:
try:
pseudo_data_settings = data['pseudo_data_settings']
except:
pass
for trial in data['trials']:
trials = process_trial(trials, trial)
data = {
'minimizer_settings': minimizer_settings,
'template_settings': template_settings,
'trials': trials
}
if pseudo_data_settings:
data['pseudo_data_settings'] = pseudo_data_settings
to_hdf(data_dict=data, tgt=args.outfile)
print "Time to process files: %s" % (datetime.now() - start_time)
print "Skipping file: ",filename
continue
if not minimizer_settings:
minimizer_settings = data['minimizer_settings']
if not template_settings:
template_settings = data['template_settings']
if not pseudo_data_settings:
try:
pseudo_data_settings = data['pseudo_data_settings']
except:
pass
for trial in data['trials']:
trials = process_trial(trials,trial)
data = {
'minimizer_settings': minimizer_settings,
'template_settings': template_settings,
'trials': trials
}
if pseudo_data_settings:
data['pseudo_data_settings'] = pseudo_data_settings
to_hdf(data_dict=data, tgt=args.outfile)
print "Time to process files: %s"%(datetime.now() - start_time)