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error in loading a fits table as a DataFrame #182

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Illuminista opened this issue Feb 9, 2022 · 9 comments
Open

error in loading a fits table as a DataFrame #182

Illuminista opened this issue Feb 9, 2022 · 9 comments

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@Illuminista
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Illuminista commented Feb 9, 2022 •
edited by giordano
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I am a rookie but it seems that something is to working as expected

from the manual:

julia> f[2]
File: file.fits
HDU: 2
Type: Table
Rows: 20
Columns: Name  Size  Type    TFORM  
         .... ....
Table HDUs implement the [Tables.jl] interface, so you can load them into other table types, like [DataFrames].
julia> df = DataFrame(f[2])

my case:

julia> f[2]
File:XXX.fits
HDU: 2
Type: Table
Rows: 24
Columns: Name               Size  Type     TFORM  
                    col1                         Float64  D   
.... ....

julia> df=DataFrame(f[2])
ArgumentError: no default `Tables.columns` implementation for type: TableHDU

Stacktrace:
 [1] columns
   @ ~/.julia/packages/Tables/M26tI/src/fallbacks.jl:264 [inlined]
 [2] DataFrame(x::TableHDU; copycols::Nothing)
   @ DataFrames ~/.julia/packages/DataFrames/BM4OQ/src/other/tables.jl:58
 [3] DataFrame(x::TableHDU)
   @ DataFrames ~/.julia/packages/DataFrames/BM4OQ/src/other/tables.jl:49
 [4] top-level scope
   @ In[17]:1
 [5] eval
   @ ./boot.jl:373 [inlined]
 [6] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:1196
@mileslucas
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Hi, thanks for the report. Can you please list your version of FITSIO.jl in this environment?

julia>] st FITSIO

@mileslucas
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I just gave this a try and did not run into any issues-

(jl_K0Xnrq) pkg> st
Status `/private/var/folders/q6/j_0w4_mx13jg_7mw9__902f40000gn/T/jl_K0Xnrq/Project.toml`
  [a93c6f00] DataFrames v1.3.2
  [525bcba6] FITSIO v0.16.12

julia> using DataFrames, FITSIO

julia> hdus = FITS("https://fits.gsfc.nasa.gov/samples/WFPC2u5780205r_c0fx.fits")
File: https://fits.gsfc.nasa.gov/samples/WFPC2u5780205r_c0fx.fits
Mode: "r" (read-only)
HDUs: Num  Name                   Type
      1                           Image
      2    u5780205r_cvt.c0h.tab  ASCIITable

julia> df = DataFrame(hdus[2]);

julia> first(df, 3)
3×49 DataFrame
 Row │ CRVAL1   CRVAL2   CRPIX1   CRPIX2   CD1_1        CD1_2        CD2_1        CD2_2        DATAMI ⋯
     │ Float64  Float64  Float64  Float64  Float64      Float64      Float64      Float64      Float6 ⋯
─────┼─────────────────────────────────────────────────────────────────────────────────────────────────
   1 │ 182.631  39.3963    420.0    424.5  -1.06704e-6  -1.25958e-5  -1.26016e-5   1.06655e-6  -73.19 ⋯
   2 │ 182.626  39.4121    423.5    414.0  -2.75605e-5   2.08221e-6   2.08021e-6   2.75871e-5  -19.95
   3 │ 182.652  39.4109    436.0    424.5   2.23913e-6   2.75426e-5   2.75684e-5  -2.23704e-6  -58.53
                                                                                     41 columns omitted

@Illuminista
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Illuminista commented Feb 28, 2022 via email

@Illuminista
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Illuminista commented Feb 28, 2022 via email

@mileslucas
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Okay, let's start with the version issue.

Can you try updating your whole environment? This should upgrade your registry.

From the REPL-mode:

julia>] up

or

julia> using Pkg
julia> Pkg.update()

Please check if this upgrades your FITSIO version. If it does not, but you see the "updating registry" message, that means some other dependency is manually restricting your FITSIO.jl version. If you do not see a message that the registry is updating, please manually try

julia>] registry up

@Illuminista
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Illuminista commented Mar 1, 2022 via email

@mileslucas
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mileslucas commented Mar 2, 2022 •
edited
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Okay, I think something is wrong with your registry, because the latest version of DustExtinction.jl (v0.11) has compatibility for FITSIO.jl v0.16.

The easiest fix is to remove the registry and let Julia fix it itself, can you give this a shot?

$ cd ~/.julia/registries
$ rm -r General*

and then from Julia (in the default, v1.7 environment)

julia>] up

@giordano
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giordano commented Mar 2, 2022

Or from within julia:

]registry rm General
registry add General

@Illuminista
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Illuminista commented Mar 2, 2022 via email

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@giordano @mileslucas @Illuminista