Hello,
For coherence I leave the original formulation in this cell but I have made a MWE in the second cell below. Thanks
I am building a package that has some dependencies including PythonCall. The module is like this:
module IntrospectiveStreams
using DataFrames, DataFramesMeta
using PolygonOps
using StaticArrays
using PythonCall
using CairoMakie, AlgebraOfGraphics
using ElectronDisplay
@py begin
import galstreams
import astropy.coordinates as coord
import astropy.units as u
import astropy.table as at
import ezmist
import gala.coordinates as galacoord
import pyia
end
export correct_extinction_Gaia,
curation!,
load_stream_track,
get_isochrone,
compute_in_self_coords!,
mask_gc!,
filter_cmd!,
filter_on_sky!,
filter_on_Ī¼_plane!,
filter_along_Ļā,
filter_along_Ļā!,
filter_with_Ļā!,
filter_PWB18!,
filter_box_on_Ī¼_plane!,
reflex_correct!,
clean_xmatch!
export plot_histog_on_sky,
plot_histog_on_sky_with_gc,
plot_histog_on_sky_self_frame,
plot_scatter_on_sky_self_frame,
plot_scatter_on_sky_Ī¼_arrows_self_frame,
plot_scatter_on_sky_Ī¼_corr_arrows_self_frame,
plot_histog_on_Ī¼_plane,
plot_histog_on_Ī¼_plane_self_frame,
plot_scatter_on_Ī¼_plane_self_frame,
plot_scatter_on_Ī¼_corr_plane_self_frame,
plot_track_on_Ī¼_corr_plane_self_frame,
plot_histog_cmd,
plot_isochrone_cmd
export correct_extinction_Gaia_loop,
basic_pipeline
include("data_methods.jl")
include("plot_methods.jl")
include("pipelines.jl")
include("run_extinction.jl")
end
Three other important parts of code are the ārun_extinction.jlā:
"""Run extinction correction for all the streams."""
name_s = ["GD-1", "Pal5", "Jhelum", "PS1-A", "Fjorm-M68"]
correct_extinction_Gaia_loop(name_s)
and two functions:
"""Extinction correction for Gaia magnitudes from Gaia dataset."""
function correct_extinction_Gaia(file_orig::String, file_corr::String)::Nothing
println(file_orig)
data = at.Table.read(file_orig)
println("done")
g = pyia.GaiaData(data)
bp0 = g.get_BP0()
rp0 = g.get_RP0()
g0 = g.get_G0()
data["bp"] = bp0
data["rp"] = rp0
data["g"] = g0
data.write(file_corr, format="fits", overwrite=true)
return nothing
end
"""Performing extinction correction for a given list of streams."""
function correct_extinction_Gaia_loop(name_s::Vector{String})
for i in 1:length(name_s)
println("Correcting extinction of stream $(name_s[i])")
host_dir = "/home/mmestre/casa/work/data/cats"
file_orig = "$(host_dir)/GaiaDR3-$(name_s[i])-all.fits"
file_corr = "$(host_dir)/GaiaDR3-$(name_s[i])-all_extincorr.fits"
correct_extinction_Gaia(file_orig, file_corr)
end
end
As presented, everything works as expected, the files are correctly processed. But I would like that the ārun_extinction.jlā file not to be included in the package. I want that action to be done from the REPL after āusing IntrospectiveStreamsā (not while using as it is now working). But it fails with this log related to PythonCall:
julia> name_s = ["GD-1", "Pal5", "Jhelum", "PS1-A", "Fjorm-M68"]
5-element Vector{String}:
"GD-1"
"Pal5"
"Jhelum"
"PS1-A"
"Fjorm-M68"
julia> correct_extinction_Gaia_loop(name_s)
Correcting extinction of stream GD-1
/home/mmestre/casa/work/data/cats/GaiaDR3-GD-1-all.fits
[922770] signal (11.1): Segmentation fault
in expression starting at REPL[7]:1
PyObject_GetAttr at /usr/local/src/conda/python-3.10.8/Objects/object.c:922
PyObject_GetAttr at /home/mmestre/.julia/packages/PythonCall/dsECZ/src/cpython/pointers.jl:299 [inlined]
macro expansion at /home/mmestre/.julia/packages/PythonCall/dsECZ/src/Py.jl:131 [inlined]
pygetattr at /home/mmestre/.julia/packages/PythonCall/dsECZ/src/abstract/object.jl:60
getproperty at /home/mmestre/.julia/packages/PythonCall/dsECZ/src/Py.jl:272
unknown function (ip: 0x7f61aeee3fd6)
_jl_invoke at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
correct_extinction_Gaia at /home/mmestre/.julia/dev/IntrospectiveStreams/src/data_methods.jl:4
correct_extinction_Gaia_loop at /home/mmestre/.julia/dev/IntrospectiveStreams/src/pipelines.jl:8
jfptr_correct_extinction_Gaia_loop_624 at /home/mmestre/.julia/compiled/v1.9/IntrospectiveStreams/ZtSfS_tWCnV.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
do_call at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/toplevel.c:856
jl_toplevel_eval_flex at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/toplevel.c:856
jl_toplevel_eval_flex at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
eval_user_input at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:153
repl_backend_loop at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:249
#start_repl_backend#46 at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:234
start_repl_backend at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:231
_jl_invoke at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
#run_repl#59 at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:379
run_repl at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:365
jfptr_run_repl_59932.clone_1 at /home/mmestre/.julia/juliaup/julia-1.9.0-rc3+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
#1017 at ./client.jl:421
jfptr_YY.1017_33143.clone_1 at /home/mmestre/.julia/juliaup/julia-1.9.0-rc3+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
jl_f__call_latest at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/builtins.c:774
#invokelatest#2 at ./essentials.jl:816 [inlined]
invokelatest at ./essentials.jl:813 [inlined]
run_main_repl at ./client.jl:405
exec_options at ./client.jl:322
_start at ./client.jl:522
jfptr__start_40741.clone_1 at /home/mmestre/.julia/juliaup/julia-1.9.0-rc3+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
true_main at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci4-4/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x401098)
Allocations: 20204319 (Pool: 20194208; Big: 10111); GC: 31
Segmentation fault
Specifically it fails exactly in the line that says: data = at.Table.read(file_orig).
I would really appreciate any help.