Starfish-develop / Starfish-develop/Starfish
gridtools - parameter assertion error
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Description
I am trying to do the first WASP14 tutorial but have not been able to generate the hdf5 data yet.
I setup config file like the docs as shown .
# YAML configuration script
name: example_wasp14
data:
grid_name: "PHOENIX"
files: ["data/WASP14/WASP14-2009-06-14.hdf5"]
instruments : ["TRES"]
orders: [22]
outdir : output/
plotdir : plots/
# The parameters defining your raw spectral library live here.
grid:
raw_path: "/home/jneal/Phd/data/fullphoenix/phoenix.astro.physik.uni-goettingen.de/HiResFITS/PHOENIX-ACES-AGSS-COND-2011/"
hdf5_path: "libraries/PHOENIX_TRES_test.hdf5"
parname: ["temp", "logg"]
key_name: "t{0:.0f}g{1:.1f}" # Specifies how the params are stored
# in the HDF5 file
parrange: [[2300, 3700], [4.0, 5.5]]
wl_range: [6300, 6360]
buffer: 50. # AA
But when I try to run the HDF5Creator code from the docs I get an Assertion Error.
import Starfish
from Starfish.grid_tools import PHOENIXGridInterfaceNoAlpha as PHOENIX
from Starfish.grid_tools import HDF5Creator, TRES
mygrid = PHOENIX()
instrument = TRES()
creator = HDF5Creator(mygrid, Starfish.grid["hdf5_path"], instrument,
ranges=Starfish.grid["parrange"])
creator.process_grid()
FFT grid stretches from 6250.000000000003 to 6409.999999999997
wl_FFT dv is 0.23127228225041102 km/s
Total of 60 files to process.
Processing [ 2300. 4.]
Traceback (most recent call last):
File "hdf5_create.py", line 14, in <module>
creator.process_grid()
File "/home/jneal/Phd/Codes/Repos/Starfish/Starfish/grid_tools.py", line 786, in process_grid
fl, header = self.process_flux(param)
File "/home/jneal/Phd/Codes/Repos/Starfish/Starfish/grid_tools.py", line 722, in process_flux
flux, header = self.GridInterface.load_flux(parameters)
File "/home/jneal/Phd/Codes/Repos/Starfish/Starfish/grid_tools.py", line 232, in load_flux
self.check_params(parameters) # Check to make sure that the keys are
File "/home/jneal/Phd/Codes/Repos/Starfish/Starfish/grid_tools.py", line 147, in check_params
assert len(parameters) == len(self.param_names)
AssertionError
If I print out Starfish.grid I get
{'hdf5_path': 'libraries/PHOENIX_TRES_test.hdf5', 'buffer': 50.0, 'key_name': 't{0:.0f}g{1:.1f}', 'parrange': [[2300, 3700], [4.0, 5.5]], 'parname': ['temp', 'logg'], 'raw_path': '/home/jneal/Phd/data/fullphoenix/phoenix.astro.physik.uni-goettingen.de/HiResFITS/PHOENIX-ACES-AGSS-COND-2011/', 'wl_range': [6300, 6360]}
I assume that these are the parameters that it is counting.
How can I resolve this issue so that I can continue on with the tutorial?
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Research direction
Reproduce the WASP14 tutorial setup using the shown YAML configuration and HDF5Creator call. Start in Starfish/grid_tools.py at HDF5Creator.process_grid, process_flux, and check_params, then compare the generated parameter values with the PHOENIX interface expectations. Done means the tutorial creates the HDF5 library without the assertion error.
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Assessment
- Tech stack
- python, yaml
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100