Reading/Writing RMEMeas Objects

This is a basic example demonstrating how to read and write a RMEMeas object.

Creating an Object

First lets create an object that we want to save.

from rmellipse.uobjects import RMEMeas

import xarray as xr
import numpy as np

nom = xr.DataArray(np.zeros((10, 2)),
                   dims=('d1', 'd2'),
                   coords={'d1': np.arange(10),
                           'd2': np.arange(2)})

meas = RMEMeas.from_nom(name='meas', nom=nom)

meas.add_umech(
    name='mymechanisms',
    value=meas.nom + np.ones(meas.nom.shape) * 0.01,
    dof=np.inf,
    category={'Type': 'B', 'Origin': 'Data Sheet'},
    add_uid=True
)

for i in range(100):
    meas.add_mc_sample(meas.nom + np.random.rand(*meas.nom.shape) * 0.01)

C:\Users\dcg2\AppData\Local\Temp\1\tmps8r3znms\d7af01cdebe95d15ae90b93035c551076e223283\docs\examples\RME_gettingstarted\plot_e03_reading_writing.py:26: DeprecationWarning: add_uid is deprecated and will be removed in 0.5.0, all umech_ids will be assigned as a uid moving. This is included to avoid breaking existing code.
  meas.add_umech(

HDF5 Saving

Saving to HDF5 is the recommended format for saving RMEMeas objects. Compared to xml, it’s much faster and preserves category and degree of freedom information about the object. In addition, the HDF5 format doesn’t require you to define a data format with to_csv and from_csv functions.

To save, open an HDF5 file or group and pass that to the rmellipse.uobjects.RMEMeas.to_h5() function. The RMEMeas object will be stored in the group you provide it under a group with it’s name. The override argument tells the function to delete any pre-existing groups with that RMEMeas objects name then try to save it, to avoid permission errors.

We recommend downloading the HDF5 viewer software. You can inspect your HDF5 object, and you will see that under the ‘myval’ group this creates, you will see the cov,mc,covdofs, and covcats attributes stored. Each one is an HDF5 representation of an xarray DataArray and together completely describe your RMEMeas object.

import h5py
with h5py.File('meas.hdf5', 'a') as f:
    meas.to_h5(f, override=True)
    print(f[meas.name])

C:\Users\dcg2\AppData\Local\Temp\1\tmps8r3znms\d7af01cdebe95d15ae90b93035c551076e223283\docs\examples\RME_gettingstarted\plot_e03_reading_writing.py:60: DeprecationWarning: to_h5() is deprecated and will be removed in 0.5.0, use rmellipse.utils.save_object instead.
  meas.to_h5(f, override=True)
<HDF5 group "/meas" (4 members)>

HDF5 Reading

You can open the HDF5 file you made in read mode, then pass in the group with it’s name to rmellipse.uobjects.RMEMeas.from_h5() in order to read it.

with h5py.File('meas.hdf5', 'r') as f:
    meas = RMEMeas.from_h5(f['meas'])
    print(meas)

C:\Users\dcg2\AppData\Local\Temp\1\tmps8r3znms\d7af01cdebe95d15ae90b93035c551076e223283\docs\examples\RME_gettingstarted\plot_e03_reading_writing.py:71: DeprecationWarning: from_h5() is deprecated and will be removed in 0.5.0, use rmellipse.utils.load_object instead.
  meas = RMEMeas.from_h5(f['meas'])
meas with nominal:
<xarray.DataArray (d1: 10, d2: 2)> Size: 160B
array([[0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.],
       [0., 0.]])
Coordinates:
  * d1       (d1) int64 80B 0 1 2 3 4 5 6 7 8 9
  * d2       (d2) int64 16B 0 1
Attributes:
    __class__.__module__:  xarray.core.dataarray
    __class__.__name__:    DataArray
    is_big_object:         True
    save_type:             DATAARRAY_SAVEABLE

XML Saving

XML format is a legacy format inherited from the original drag and drop menu Microwave Uncertainty Framework. It is included for backwards compatibility purposes, but it is not the recommended way to save if you can help it. Specifically be aware that saving data to XML you will lose degrees of freedom and category information about your linear uncertainty mechanisms. The default degrees of freedom for linear uncertainties is infinite, and the default category for uncertainties is type B. So if you save to XML then read it back in, all your mechanisms will default to both of those properties. To preserve categories and degrees of freedom you assigned, use HDF5. Additionally, it is much slower than the HDF5 format.

To save to XML you need to define a read/write functions.

First we turn our object into the s1p_ri format using the rmellipse.dataformats.as_format()

from rmellipse.propagators import RMEProp

def to_txt(data, path):
        np.savetxt(path, data.values, delimiter=',')

def from_txt(path):
    values = xr.DataArray(np.loadtxt(path, float, delimiter=','))
    return values

m1 = RMEMeas.from_nom('mymeas', xr.DataArray(np.zeros((2,2))))
m1.add_umech('my umech', m1.nom.copy()+0.1)

m1.to_xml(
    '.',
    to_txt,
    data_extension='.csv',
    header_extension='.meas'
)

Once we have our measurement in a format with read/write functions defined we can use the rmellipse.uobjects.RMEMeas.to_xml() and rmellipse.uobjects.RMEMeas.from_xml() functions.

rmellipse.uobjects.RMEMeas.to_xml() is expecting a target directory to save the measurement in. It will save a header ‘.meas’ file and a ‘…_Support’ in that directory with the covariance and Monte Carlo data next to it. Both will be named using the RMEMeas object’s name attribute. When a RMEMeas object is passed through a function, it’s name attribute is changed to the name of that function. So, be sure to change the name attribute to something useful if the function name is not specific enough.

m2 = RMEMeas.from_xml(
    'mymeas.meas',
    from_csv=from_txt
)
assert (m2.cov.values == m1.cov.values).all()