load_omas_imas breaks if data_error_{upper, lower} not filled correctly

[jsferreira]

Dear All,

I was trying to read a set of IDS which contains data_error_{upper, lower} nodes that are not filled correctly. When OMAS tries to build an uarray (uncertainties) it will throw na exception NegativeStdDev: The standard deviation cannot be negative
breaking the load process. Could we add an option to just give a warning in those cases. Errors would be ignored. Actually this should be the default behaviour otherwise it can be a bummer for the user.
I am using omas version 0.29

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/afs/gw/switm/omfit/atom/omas/omas/omas_imas.py", line 456, in load_omas_imas
    data = uarray(data,stdata)
  File "/gw/switm/omfit/atom/miniconda2/lib/python2.7/site-packages/uncertainties/unumpy/core.py", line 287, in uarray
    (nominal_values, std_devs))
  File "/gw/switm/omfit/atom/miniconda2/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2576, in __call__
    return self._vectorize_call(func=func, args=vargs)
  File "/gw/switm/omfit/atom/miniconda2/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2652, in _vectorize_call
    outputs = ufunc(*inputs)
  File "/gw/switm/omfit/atom/miniconda2/lib/python2.7/site-packages/uncertainties/unumpy/core.py", line 286, in <lambda>
    lambda v, s: uncert_core.Variable(v, s), otypes=[object])
  File "/gw/switm/omfit/atom/miniconda2/lib/python2.7/site-packages/uncertainties/core.py", line 2585, in __init__
    self.std_dev = std_dev  # Assignment through a Python property
  File "/gw/switm/omfit/atom/miniconda2/lib/python2.7/site-packages/uncertainties/core.py", line 2606, in std_dev
    raise NegativeStdDev("The standard deviation cannot be negative")
uncertainties.core.NegativeStdDev: The standard deviation cannot be negative

[jsferreira]

@orso82, thanks for the quick fix.

[orso82]

You are welcome! Glad to see OMAS is getting used! 👍