Description

Cannot install agama on GitHub and RTD VMs for testing optional dependencies

See also GalacticDynamics-Oxford/Agama#8

Expected behavior

To be able to pip install agama and have the c code compile

Actual behavior

It fails. See GalacticDynamics-Oxford/Agama#8

Steps to Reproduce

Add agama to optional dependencies in setup.cfg and push to GitHub.

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• Please check that the development version still produces the same bug. You can install development version with pip install git+https://github.com/astropy/astropy command.

Description

Get the coefficients in repeated runs and find the correlations!

Additional context

For agama multipole

``the coefficients are indeed written to text files by the Potential.export() method, though the detailed specification of this file is not given in the docs. But it does have a rather simple structure: after a few header lines, there comes an array of potential coefficients, followed by radial derivative coefficients: Phi_{lm}(r), dPhi_{lm}/dr. Each line contains the radius and then the values of each potential harmonic at this radius, in the following order: l=0; l=1,m=-1; l=1,m=0; l=1,m=1; l=2,m=-2; l=2,m=-1; etc., where negative m correspond to sine and positive - to cosine terms in the expansion - in total, (lmax+1)^2 terms. The normalization convention is described in the section A.4.1 of reference.pdf
Although there is no way to access these coefs from Python, you may save them to a file and read it off as a numpy array if needed." Eugene Vasiliev (GalacticDynamics-Oxford/Agama#9)

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Description

Currently the Measurer classes resample in a specific frame, but return to the user the data transformed back into the input frame. It would be better for the user and debugging purposes if it returned in the re-sampling frame.

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Plot of reduced chi-square (or similar statistic) for how well a SCF fits the spiral arms potential as a function of Nmax/Lmax

Description

Subclass MeasurementErrorSampler to make a InterpolatedGridMeasurementErrorSampler that takes a catalog of data points, for example Gaia, takes the errors and creates a 3D interpolated & smoothed grid of the errors as a function of the position. This can be evaluated with the MeasurementErrorSampler given positions from the PotentialSampler class to create realistic measurement errors.

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Description

Instead of wrapping a galpy potential in a galpy DF class before passing to PotentialSampler, have PotentialSampler be able to automatically determine the correct match. This could be a simple JSON registry.

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Description

Figure out why and solve!

Expected behavior

• dependent on l, m max
• dependent on the grid

Actual behavior

• dependent on l, m max : it's not
• dependent on the grid : maybe it is?

Steps to Reproduce

# THIRD PARTY
import agama
import astropy.coordinates as coord
import astropy.units as u
import numpy as np
from astropy.visualization import quantity_support
from galpy import df as gdf
from galpy import potential as gpot

# PROJECT-SPECIFIC
from discO import (
    GaussianMeasurementErrorSampler,
    PotentialFitter,
    PotentialSampler,
    conf,
)
from discO.plugin.agama.fitter import (
    AGAMAMultipolePotentialFitter,
    AGAMAPotentialFitter,
)
from discO.core.pipeline import Pipeline
from discO.core.residual import GridResidual

quantity_support();

mass = 1e12 * u.solMass
r0 = 10 * u.kpc  # scale factor

agama.setUnits(mass=1, length=1, velocity=1)

hernquist_pot = gpot.HernquistPotential(amp=2 * mass, a=r0)
sampler = PotentialSampler(gdf.isotropicHernquistdf(hernquist_pot))
measurer = GaussianMeasurementErrorSampler(c_err=1*u.percent)  # 10% error
fitter = PotentialFitter(None, key="agama", pot_type="multipole", symmetry="s", gridsizeR=50, lmax=0, mmax=0)

_x = np.linspace(-5, 5, num=50)
x, y, z = np.meshgrid(_x, _x, _x) * u.kpc
points = coord.CartesianRepresentation(x, y, z)
residualer = GridResidual(points, original_pot=hernquist_pot)

pipe = Pipeline(sampler=sampler, fitter=fitter, residualer=residualer)
pipe

resid = pipe(n=10000, frame=coord.Galactocentric(), random=0)


from mpl_toolkits.mplot3d import axes3d
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import numpy as np

fig = plt.figure()
ax = fig.gca(projection='3d')

rar = np.abs(resid.represent_as(coord.SphericalRepresentation).vf_distance.flatten().value)
norm = mpl.colors.Normalize(vmin=min(rar), vmax=max(rar), clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap=cm.inferno_r)

uvw = resid.vf_xyz.value * 1e13

qv = ax.quiver(
    x, y, z, *uvw,
    color=mapper.to_rgba(rar, alpha=0.1),
    length=0.1, )
ax.set_xlim(-8, 8)
ax.set_ylim(-8, 8)
ax.set_zlim(-8, 8)

plt.colorbar(qv)

plt.show()

System Details

macOS-10.16-x86_64-i386-64bit
Python 3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 07:56:27)
[Clang 9.0.1 ]
astropy 4.3.dev310+g59d625df4.d20201220
astroquery 0.4.2.dev6458
Matplotlib 3.2.1
Numpy 1.18.4
Scipy 1.4.1

Checklist

• Check out our contributing guidelines.
• Check out our code of conduct.
• Search the GitHub repository to see if a similar issue has already been posted. If a similar issue is closed, have a quick look to see if you are satisfied by the resolution. If not please go ahead and open an issue!
• Please check that the development version still produces the same bug. You can install development version with pip install git+https://github.com/astropy/astropy command.

Description

Need to save chains and plot them. Want to save chains as we go. Emcee has a nice thing going.

https://emcee.readthedocs.io/en/stable/tutorials/monitor/

Checklist

• Check out our contributing guidelines.
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@CCAstro35, as we discussed, we won't add the actual SIM data. Once I have the data file (can you email me the Google Drive link) we can set up the folder structure and correct .gitignore. Then we can close this issue.

Need to add a template for PRs.

Description

Currently the mass and potential are embedded in a SkyCoord. This does not work very well as any operation that returns a new instance, like reshape means that the attributes need to be reassigned (separately reshaped).

Possible fixes:

• Subclass SkyCoord, with hooks to properly maintain these attributes
• embed in a table (SkyCoord is a valid mixin) ... but can tables be stacked depth-wise?
• Xarray? but how does that deal with SkyCoords?

Checklist

• Check out our contributing guidelines.
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Many of the links are broken. The CI and codecov links especially.

Description

Get these fitters working.

The SCF implementation doesn't seem to work. The errors are quite large.

Need the N-Body PR in galpy: jobovy/galpy#444

Additional context

Checklist

• Check out our contributing guidelines.
• Check out our code of conduct.
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Question

Help with Units! I'm trying to figure out how to get AGAMA functions to output units!

From the documentation pdf on AGAMA/doc

@CCAstro35 If you're familiar with this, could you send me a snippet of example code?

Description

#20 Needs documentation, docstrings, and examples.

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Description

Like agama Multipole fitter, but CylSpline.

Additional context

Checklist

• Check out our contributing guidelines.
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Determine what physical resolution roughly corresponds to each Nmax/Lmax