Looks like something has gotten screwed up in the Polynomial fitting routine

0th Transfer matrix looks like:

[[1, -2.77555756156289e-17, 5.55111512312578e-17, 5.55111512312578e-17, 5.55111512312578e-17, 4.44089209850063e-16],
[1.89735380184963e-19, 1.0000000004124, 1.33229261702213e-15, 1.33229261702213e-15, 1.33229219350566e-15, 2.85638203492483e-12],
[-1.06581410364015e-14, -1.77635683940025e-15, 0.999999999999998, -2.22044604925031e-15, -2.66453525910038e-15, -2.1316282072803e-14],
[-1.81898940354586e-12, -5.6843418860808e-14, 0, 199.007437936864, 0, 0],
[2.8421709430404e-14, 0, 1.33226762955019e-15, 1.33226762955019e-15, 1, 1.06581410364015e-14],
[6.25277607468888e-13, -1.4210854715202e-14, 7.105427357601e-15, 7.105427357601e-15, 0, 199.990000644285]]

This should be close to unity.

Going through possible changes that might affect the optics calculations....could it be related to the changes at:
http://bazaar.launchpad.net/~maus-maintainers/maus/merge/revision/600.1.165 ?
e.g.
http://bazaar.launchpad.net/~maus-maintainers/maus/merge/revision/600.1.165#src/common_cpp/Optics/CovarianceMatrix.cc

I also see a related change was made to the envelope tool plotter:
http://bazaar.launchpad.net/~maus-maintainers/maus/merge/revision/1023.1.3#bin/utilities/envelope_tool/lib/plotter.py

I noticed that the list of primaries is incorrect and will not cancel errors from first derivatives...

Found another issue - PolynomialOpticsModel::CalculateTransferMap is using x' on input and px on output, which fails to fit properly.

Email to users:

Apologies for the slow reply, I was at KURRI and then on vacation.

There was a bug introduced on 28th January, which means that the optics routines do not correctly normalise the momentum vector when calculating beta functions.

The workaround is to normalise the momentum by hand in the optics example script. This can be done by modifying line 117 of

bin/examples/optics_examples/match_step_4_beta_function.py

to replace the line

          "momentum":{"x":0.0, "y":0.0, "z":1.0}

with the line

          "momentum":{"x":0.0, "y":0.0, "z":self.mom}

I checked this against MAUS-v0.8.2. I attach output plots from the fixed code. I will try to get a full fix in ASAP.

This will affect versions MAUS-v0.7.7 through MAUS-v0.8.2. Apologies for any inconvenience caused. Please don't hesitate to ask if you have further problems.