def save_txt(fname='nda.txt', arr=None, cmts=(), fmt='%.1f', verbos=False, addmetad=True) :
"""Save n-dimensional numpy array to text file with metadata.
- fname - file name for text file,
- arr - numpy array,
- cmts -list of comments which will be saved in the file header.
"""
#recs = ['# %03d %s' % (i,cmt) for i, cmt in enumerate(cmts)]
recs = ['# %s' % cmt for cmt in cmts]
recs.append('\n# HOST %s' % gu.get_hostname())
recs.append('# WORK_DIR %s' % gu.get_cwd())
recs.append('# FILE_NAME %s' % fname)
recs.append('# DATE_TIME %s' % gu.str_tstamp(fmt='%Y-%m-%dT%H:%M:%S'))
recs.append('# UID %s' % gu.get_login())
recs.append('# SHAPE %s' % str(arr.shape).replace(' ',''))
recs.append('# DATATYPE %s' % str(arr.dtype))
if addmetad :
recs.append('\n# DTYPE %s' % str(arr.dtype))
recs.append('# NDIM %s' % len(arr.shape))
for i in range(len(arr.shape)) :
recs.append('# DIM:%d %s' % (i, arr.shape[i]))
arr2d = nu.reshape_nda_to_2d(arr)
# pretty formatting
recs.append('' if len(arr.shape)>1 else '\n')
nline = '\n' if len(arr.shape)>1 else ' '
hdr = '\n'.join(recs)
#print(hdr)
np.savetxt(fname, arr, fmt, delimiter=' ', newline=nline, header=hdr, comments='') #, footer='\n') #, comments='# ')
if verbos : print('File %s is saved' % fname)
def set_metadata_values(self):
"""Sets metadata values associated with self.data_nda
"""
logger.debug('in set_metadata_values')
model = self.model
nda = self.data_nda
colk, colv = 0, 1
for row in range(model.rowCount()):
key = model.item(row, colk).text()
if key == 'data_size': model.item(row, colv).setText(str(nda.size))
elif key == 'data_dtype':
model.item(row, colv).setText(str(nda.dtype))
elif key == 'data_ndim':
model.item(row, colv).setText(str(nda.ndim))
elif key == 'data_shape':
model.item(row, colv).setText(str(nda.shape))
elif key == 'host':
model.item(row, colv).setText(gu.get_hostname())
elif key == 'uid':
model.item(row, colv).setText(gu.get_login())
elif key == 'cwd':
model.item(row, colv).setText(gu.get_cwd())
logger.info('Model document content:\n %s\n%s' %
(self.info_model_dicdoc(),
info_ndarr(self.data_nda, 'data n-d array ')))
def msg_to_log(runs=[]):
"""Returns (str) message to the log file for list of (str) runs.
"""
if len(runs) == 0: return None
tstamp = gu.str_tstamp('%Y-%m-%dT%H:%M:%S', time())
login = gu.get_login()
cwd = gu.get_cwd()
host = gu.get_hostname()
cmd = sys.argv[0].split('/')[-1]
recs = [
'%s %s %s %s cwd:%s cmd:%s' % (s, tstamp, login, host, cwd, cmd)
for s in runs
]
text = '\n'.join(recs)
return text + '\n'
def _history_record(dcmts):
"""Returns history record made of dictionary comments and system info
"""
user = gu.get_login()
host = gu.get_hostname()
tstamp = gu.str_tstamp(fmt='%Y-%m-%dT%H:%M:%S zone:%Z')
rnum = '%04d' % dcmts.get('run')
exp = '%s' % dcmts.get('exp')
ifname = '%s' % dcmts.get('ifname')
ofname = '%s' % dcmts.get('fname')
app = '%s' % dcmts.get('app')
cmt = '%s' % dcmts.get('comment')
return 'file:%s copy_of:%s exp:%s run:%s app:%s user:%s host:%s cptime:%s comment:%s\n' % \
(ofname.ljust(14),
ifname,
exp.ljust(8),
rnum.ljust(4),
app.ljust(10),
user,
host,
tstamp.ljust(29),
cmt)
def docdic(data, dataid, **kwargs):
"""Returns dictionary for db document in style of JSON object.
"""
doc = {
'experiment': kwargs.get('experiment', None),
'run': kwargs.get('run', '0'),
'run_end': kwargs.get('run_end', 'end'),
'detector': kwargs.get('detector', None),
'ctype': kwargs.get('ctype', None),
'time_sec': kwargs.get('time_sec', None),
'time_stamp': kwargs.get('time_stamp', None),
'version': kwargs.get('version', 'v00'),
'comment': kwargs.get('comment', ''),
'extpars': kwargs.get('extpars', None),
'uid': gu.get_login(),
'host': gu.get_hostname(),
'cwd': gu.get_cwd(),
'id_data': dataid,
}
if isinstance(data, np.ndarray):
doc['data_type'] = 'ndarray'
doc['data_dtype'] = str(data.dtype)
doc['data_size'] = '%d' % data.size
doc['data_ndim'] = '%d' % data.ndim
doc['data_shape'] = str(data.shape)
elif isinstance(data, str):
doc['data_type'] = 'str'
doc['data_size'] = '%d' % len(data)
else:
doc['data_type'] = 'any'
logger.debug('doc data type: %s' % doc['data_type'])
return doc