spacetelescope / pandeia-coronagraphy Goto Github PK

Hello,

I have been testing the MIRI SGD notebook and running into issues when generating the KLIP reference. This is related to uncorrected nan's in the SGD reference images, possibly due to saturation artifacts, that cause the code to crash.

Here's what is in the original code -

reg = analysis.register_to_target(slope,target_slope,rescale_reference=True)
sgd_reg.append(reg)
sgd_reg = np.array(sgd_reg) 

I modified it in the following manner -

slope[np.isnan(slope)] = 0
reg = analysis.register_to_target(slope,target_slope,rescale_reference=True)
sgd_reg.append(reg) 

This does result in the central PSF artifact not getting completely removed in the target-reference but that could be corrected by drawing a mask on the central 0.1-0.2 arcsec.

Folks,

I think if a bug has been introduced by the newer version of pandeia.engine (1.2). I've been running the various notebooks here, but always get the error
UnsupportedError: Multiple dithers for imaging is not yet supported
when the calculation is attempted (i.e. in calculate_batch).

Installing pandeia.engine-1.1.1 seems to solve this issue, and with 1.2 I can successfully run the quickstart notebook from pandeia-tutorials, so my installs seem OK.

I'm not at all familiar with the inner workings on pandeia, so I haven't been able to figure out what the problem actually is and don't have any suggestions sorry!

cheers
Grant

In the Installation section:

• Update the repository URL from github.com/kvangorkom/ to github.com/spacetelescope/ in the pip commands (2 instances).
• Use python 3.x instead of 2.7 in the conda create command.

Check for other outdated information.

If the VERSION file is missing, from installing by hand the following lines in __init__.py prevent importing jwst_pancake

try:
    version_file = os.path.join(os.path.split(__file__)[0], "VERSION")
    with open(version_file, "r") as inf:
        __version__ = inf.readline().strip()
except Exception as e:
    sys.err.write("Unable to find pancake version file!\n")

sys.err should be replaced by sys.stderr

I've just noticed what I believe is a sign error in the fourier_shift function:

Why is there a negative sign on the y shift but not on the x shift?

Note, this is a benign error if you avoid calling fourier_shift directly and instead invoke it through the register_to_target function (since the optimization in that function just solves for the required value with that sign error). But it's confusing if you try to directly access the fourier_shift function, or even if you just look at the output shifts as reported from register_to_target as a sanity check.

Copying here from kvangorkom/pandeia-coronagraphy#13:

When the Pandeia library PSFs are generated, the requested offsets for the PSFs are forced to nearest integer upsampled pixel, and then recentered by a simple pixel remapping after the call to WebbPSF (so the convolution kernel created from the PSF is centered). For on-the-fly PSFs, I've intentionally avoided forcing the offset to an integer multiple of the upsampled pixel, since we care (particularly for MIRI) about small changes to these spatially-dependent PSFs. However, the pixel remapping approach then has the side effect of producing a slightly off-center convolution kernel.

Possible mitigation strategies: interpolate the PSF for the centering step (I really don't want to do this), or adopt a higher upsampling value.

Hello,

I noticed that the PSFs appear to have different morphology depending on whether you use the pre-computed version or the webbpsf version. I've attached a figure showing the difference.

All other parameters are kept consistent between the two calls.

Copying here from kvangorkom/pandeia-coronagraphy#10

Tyler Desjardins mentions that we should consider moving emails from help[at]stsci.edu to point to the web portal where possible and appropriate. For HST (or any non-JWST), it is https://hsthelp.stsci.edu . For JWST, it is https://jwsthelp.stsci.edu . Please update info in setup.py, setup.cfg, documentation, etc as appropriate.

Please close this issue if it is irrelevant to your repository. This is an automated issue. If this is opened in error, please let pllim know!

xref spacetelescope/hstcal#317

Right now in addition to master, this repo has several branches: cache, contrasts, nircam_offsets, and pandeia1.1. I just checked and all of these appear to have already been merged into master at various points in the past; as far as I can tell there are no new commits on any of them.

Since they're already merged, I think they can & should be deleted at this point. Any objections?

I was hoping to use one of the example notebooks (nircam_photon_noise_and_contrast.ipynb) to create a slope image, but I think there might have been an update to the pandeia engine that is causing an error in the notebook now. The error is below. Is there any way I could get an updated example notebook? I can't figure out a workaround for the geometries error because I don't know what the original code looked like.

`---------------------------------------------------------------------------
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia_coronagraphy/engine.py", line 96, in perform_calculation
results = pandeia_calculation(calcfile)
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia/engine/perform_calculation.py", line 39, in perform_calculation
report = calculate_sn(calc_input, webapp=webapp)
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia/engine/etc3D.py", line 1230, in calculate_sn
scene = Scene(input=scene_configuration, webapp=webapp)
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia/engine/scene.py", line 54, in init
self._from_list(input)
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia/engine/scene.py", line 91, in _from_list
self.sources.append(src.Source(config=s, webapp=self.webapp))
File "/Users/acanipe/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia/engine/source.py", line 223, in init
if self.shape['geometry'] in self.geometries:
AttributeError: 'Source' object has no attribute 'geometries'
"""

The above exception was the direct cause of the following exception:

AttributeError Traceback (most recent call last)
in ()
1 engine.options.wave_sampling = 20
----> 2 targ_results, ref_results = engine.calculate_batch([target,reference])

~/miniconda3/envs/astroconda/lib/python3.5/site-packages/pandeia_coronagraphy/engine.py in calculate_batch(calcfiles, nprocesses)
66 nprocesses = mp.cpu_count()
67 pool = mp.Pool(processes = nprocesses)
---> 68 results = pool.map(perform_calculation, calcfiles)
69 pool.close()
70 pool.join()

~/miniconda3/envs/astroconda/lib/python3.5/multiprocessing/pool.py in map(self, func, iterable, chunksize)
264 in a list that is returned.
265 '''
--> 266 return self._map_async(func, iterable, mapstar, chunksize).get()
267
268 def starmap(self, func, iterable, chunksize=None):

~/miniconda3/envs/astroconda/lib/python3.5/multiprocessing/pool.py in get(self, timeout)
642 return self._value
643 else:
--> 644 raise self._value
645
646 def _set(self, i, obj):

AttributeError: 'Source' object has no attribute 'geometries'`

Thanks for the help!
Alicia