Comments (9)
There are at least two new file formats: .rrlvl
and .auto
. Need to find out more about how these are used and how to parse them.
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Additionally, there appears to have been a change in the fe_10.drparams
file format as the current drparams parser fails when trying to parse it with the following exception,
ValueError Traceback (most recent call last)
<ipython-input-4-e2ac303935f6> in <module>
----> 1 build_hdf5_dbase('/Users/willbarnes/Downloads/CHIANTI_9.0.1_data','/Users/willbarnes/Desktop/chianti-v9.0.1.h5',ask_before=False)
~/Documents/work/codes/fiasco/fiasco/util/setup_db.py in build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, ask_before)
76 log.debug(f'Parsing file {af}')
77 parser = fiasco.io.Parser(af, ascii_dbase_root=ascii_dbase_root)
---> 78 df = parser.parse()
79 if df is None:
80 log.warn(f'Not including {af} in {hdf5_dbase_root}')
~/Documents/work/codes/fiasco/fiasco/io/generic.py in parse(self)
48 break
49 else:
---> 50 self.preprocessor(table, line, i)
51
52 df = QTable(data=list(map(list, zip(*table))), names=self.headings)
~/Documents/work/codes/fiasco/fiasco/io/sources/ion_sources.py in preprocessor(self, table, line, index)
294 else:
295 if self._drparams_filetype == 1:
--> 296 tmp = np.array(line[2:],dtype=float)
297 if index%2 == 0:
298 tmp_col = table[-1]
ValueError: could not convert string to float: 'Badnell,'
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ping @fluxtransport
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Ok the reason these fail to parse is because the parser expects the footer, which contains the reference and other info about the data, to be fenced by -1
values, e.g. the fe_12.drparams
file looks like,
1
26 12 1.3870e+03 1.0480e+04 3.9550e+04 1.4610e+05 4.0100e+05 7.2080e+05 0.0000e+00 0.0000e+00 0.0000e+00
26 12 1.0740e-03 6.0800e-03 1.8870e-02 2.5400e-02 7.5800e-02 2.7730e-01 0.0000e+00 0.0000e+00 0.0000e+00
-1
%file: fe_12.drparams
%parameters for dielectronic recombination rate coefficients
Determined from the coefficients listed at:
http://amdpp.phys.strath.ac.uk/tamoc/DATA/RR/
These calculations have been performed by a collaboration of researchers at:
Auburn University, Rollins College, and the University of Strathclyde.
produced for the CHIANTI atomic database for astrophysical spectroscopy
created by Ken Dere (GMU): Wed Feb 15 11:13:10 2012
-1
but in the Fe X and XI drparams files, the initial -1
is missing so it tries to parse the footer as the data which obviously fails. It may be possible to just add an additional check for %file
for denoting the footer.
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This posting on the CHIANTI mailing list may be of some help.
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things are a little different with the .drparams files. the number at the beginning of the file tell what type of data it expects and from this the format of the parameters is know. So, the -1 is not really necessary
from fiasco.
Fair point. I was using the -1
as a general marker across all file types to denote the footer.
from fiasco.
See #48
from fiasco.
This posting better enumerates the needed changes: https://groups.google.com/g/chianti/c/hzJyjhkAhAw
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Related Issues (20)
- Atomic database guide in docs needs more fleshing out
- Unskip doctests in Quick Start guide
- Review documentation HOT 3
- hasattr not working with missing dielectronic properties HOT 2
- Add calculation of dielectronic level populations
- README needs updating HOT 1
- Provide guidance on use of interpolation methods HOT 3
- Add a cli tool for plotting ionization fractions
- Add an IDL comparison test for the two-photon continuum
- Incorporate dielectronic ions into two-photon continuum
- Substitute `.splups` files for `.scups` files in functions for older versions of the database HOT 2
- Type hints for functions HOT 4
- f-f scaling with temperature? HOT 4
- IDL Contribution function comparisons need to be multiplied by 0.83
- Ionization equilbirium and nonequilibrium example gallery entries should use Fe
- New numpy release (v2.0.0) causing issues? HOT 1
- Benchmarking database construction
- Add labels for running different versions of the tests
- Reconcile differences in two-photon continuum with IDL results
- Differing behavior on two different systems HOT 3
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