UnboundLocalError when calling baseline() function

[Matheus-gif]

Hey guys, thank you all very much for the package. I'm trying to replicate the baselines_examples on the notebook. I'm able to use all the function methods except for "gcvspline". I've create a virtual environment and ran the following

pkg] add PyCall
julia> using PyCall
julia> @pyimport pip
julia> pip.main(["install","rampy"])

julia> pip.main(["install", "rampy"])
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Requirement already satisfied: rampy in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (0.5.3)
Requirement already satisfied: numpy>=1.12 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from rampy) (2.2.4)
Requirement already satisfied: scipy in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from rampy) (1.15.2)
Requirement already satisfied: scikit-learn in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from rampy) (1.6.1)
Requirement already satisfied: pandas in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from rampy) (2.2.3)
Requirement already satisfied: xlrd in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from rampy) (2.0.1)
Requirement already satisfied: matplotlib in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from rampy) (3.10.1)
Requirement already satisfied: contourpy>=1.0.1 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (1.3.1)
Requirement already satisfied: cycler>=0.10 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (4.56.0)
Requirement already satisfied: kiwisolver>=1.3.1 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (1.4.8)
Requirement already satisfied: packaging>=20.0 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (24.2)
Requirement already satisfied: pillow>=8 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (11.1.0)
Requirement already satisfied: pyparsing>=2.3.1 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (3.2.1)
Requirement already satisfied: python-dateutil>=2.7 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from matplotlib->rampy) (2.9.0.post0)        
Requirement already satisfied: pytz>=2020.1 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from pandas->rampy) (2025.1)
Requirement already satisfied: tzdata>=2022.7 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from pandas->rampy) (2025.1)
Requirement already satisfied: joblib>=1.2.0 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from scikit-learn->rampy) (1.4.2)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from scikit-learn->rampy) (3.6.0)
Requirement already satisfied: six>=1.5 in c:\users\user\.julia\conda\3\x86_64\lib\site-packages (from python-dateutil>=2.7->matplotlib->rampy) (1.17.0)
0

But I'm still unable to run the notebook examples regarding baseline() on VSCode. All methods work except for "gcvspline".

# We define the portions of the spectra where we want to fit the signal background.
# roi should be an n x 2 array, see documentation at 
roi = [0 100.;200 220;280 290;420 430; 480 500]

# caling the baseline function with a natural spline that will fit the signal in ROIs
y_gcvspl, bas_gcvspl = baseline(x,y,roi,"gcvspline",s=1.)

# using the ALS algorithm (Baek et al. 2015), 10^2-10^5 lambda and 0.001-0.1 p values are recommended
y_als, bas_als = baseline(x,y,roi,"als",p=0.01,lam=10^6,niter=10)

# using the arPLS algorithm (Baek et al. 2015)
y_arpls, bas_arpls = baseline(x,y,roi,"arPLS",p=0.1,lam=10.0^6)

figure()

# plotting the initial signal and the roi
plot(x,y,"black",label="signal")

# plotting the baselines
plot(x,bas_gcvspl,"cyan",label="gcvspline")
plot(x,bas_als,"purple",linestyle="--",label="ALS")
plot(x,bas_arpls,"orange",linestyle="-.",label="arPLS")
legend()

xlabel("X",fontname="Arial",fontsize=18)
ylabel("Y",fontname="Arial",fontsize=18)

display(gcf())

PyError ($(Expr(:escape, :(ccall(#= C:\Users\User\.julia\packages\PyCall\1gn3u\src\pyfncall.jl:43 =# @pysym(:PyObject_Call), PyPtr, (PyPtr, PyPtr, PyPtr), o, pyargsptr, kw))))) <class 'UnboundLocalError'>
UnboundLocalError("cannot access local variable 'gcvspline' where it is not associated with a value")
  File "C:\Users\User\.julia\conda\3\x86_64\Lib\site-packages\rampy\baseline.py", line 149, in baseline
    c, wk, ier = gcvspline(yafit[:,0],yafit[:,1],np.sqrt(np.abs(yafit[:,1])),splinesmooth,splmode = 1) # gcvspl with mode 1 and smooth factor
                 ^^^^^^^^^


Stacktrace:
  [1] pyerr_check
    @ C:\Users\User\.julia\packages\PyCall\1gn3u\src\exception.jl:75 [inlined]
  [2] pyerr_check
    @ C:\Users\User\.julia\packages\PyCall\1gn3u\src\exception.jl:79 [inlined]
  [3] _handle_error(msg::String)
    @ PyCall C:\Users\User\.julia\packages\PyCall\1gn3u\src\exception.jl:96
  [4] macro expansion
    @ C:\Users\User\.julia\packages\PyCall\1gn3u\src\exception.jl:110 [inlined]
  [5] #107
    @ C:\Users\User\.julia\packages\PyCall\1gn3u\src\pyfncall.jl:43 [inlined]
  [6] disable_sigint
    @ .\c.jl:167 [inlined]
  [7] __pycall!
    @ C:\Users\User\.julia\packages\PyCall\1gn3u\src\pyfncall.jl:42 [inlined]
  [8] _pycall!(ret::PyObject, o::PyObject, args::Tuple{Vector{Float64}, Vector{Float64}, Matrix{Float64}, String}, nargs::Int64, kw::PyObject)
    @ PyCall C:\Users\User\.julia\packages\PyCall\1gn3u\src\pyfncall.jl:29
  [9] _pycall!(ret::PyObject, o::PyObject, args::Tuple{Vector{Float64}, Vector{Float64}, Matrix{Float64}, String}, kwargs::@Kwargs{polynomial_order::Int64, s::Float64, lam::Int64, niter::Int64, p0_exp::Vector{Float64}, p0_log::Vector{Float64}})
    @ PyCall C:\Users\User\.julia\packages\PyCall\1gn3u\src\pyfncall.jl:11
 [10] (::PyObject)(::Vector{Float64}, ::Vararg{Any}; kwargs::@Kwargs{polynomial_order::Int64, s::Float64, lam::Int64, niter::Int64, p0_exp::Vector{Float64}, p0_log::Vector{Float64}})
    @ PyCall C:\Users\User\.julia\packages\PyCall\1gn3u\src\pyfncall.jl:86
 [11] baseline(x::Vector{Float64}, y::Vector{Float64}, roi::Matrix{Float64}, basetype::String; polynomial_order::Int64, s::Float64, lam::Int64, p::Float64, ratio::Float64, niter::Int64, p0_exp::Vector{Float64}, p0_log::Vector{Float64})
    @ Spectra C:\Users\User\.julia\packages\Spectra\gifVq\src\baseline.jl:86
 [12] top-level scope
    @ c:\Users\User\Desktop\tratar_dados\codigos_julia\doutorado\dems\jl_notebook_cell_df34fa98e69747e1a8f8a730347b8e2f_X15sZmlsZQ==.jl:6

[charlesll]

Could you try installing gcvspline in Python via pip.main(["install","gcvspline"]), and tell me if this solves the problem?

Indeed, since a few years gcvspline is not installed automatically as part of Rampy, because you need a running Fortran compiler for gcvspline and this was creating problems for people working on Windows computers in particular. As not everyone was interested to use gcvspline in Rampy, I used that as a quick workaround to avoid failling the install of rampy and Spectra due to gcvspline.

[Matheus-gif]

Sure, thank you for your reply. It didn't appear to work

julia> using PyCall

julia> PyCall.pyimport("pip")["main"](["install", "gcvspline"])
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
WARNING: Ignoring invalid distribution ~atplotlib (C:\Users\User\.julia\conda\3\x86_64\Lib\site-packages)
Collecting gcvspline
  Using cached gcvspline-0.5.tar.gz (344 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [18 lines of output]
      Traceback (most recent call last):
        File "C:\Users\User\.julia\conda\3\x86_64\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 389, in <module>
          main()
        File "C:\Users\User\.julia\conda\3\x86_64\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\User\.julia\conda\3\x86_64\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 143, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\User\AppData\Local\Temp\pip-build-env-k622yh79\overlay\Lib\site-packages\setuptools\build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\User\AppData\Local\Temp\pip-build-env-k622yh79\overlay\Lib\site-packages\setuptools\build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "C:\Users\User\AppData\Local\Temp\pip-build-env-k622yh79\overlay\Lib\site-packages\setuptools\build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 1, in <module>
      ModuleNotFoundError: No module named 'numpy.distutils'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
1

[charlesll]

Thanks for the report.

This is not related to Spectra but to the installation of gcvspline by pip. Probably it uses Numpy 2.0 and I must admit I did not yet test gcvspline using this new numpy version. It may not work if they removed the distutils (required to compile the Fortran code, etc.).

Also, even if you setup numpy < 2.0, do you have a Fortran compiler on your Windows PC? This usually creates lots of issues with gcvspline. This is why it was always an optional package for Spectra and Rampy...

Anyway, I will dig into that on my side, and see if I can find the source of this error and fix the installation. Another option is to ditch the Python dependency and use my gcvspl package.

Meanwhile, I suggest you use the unispline. It already can do a pretty decent job.

[charlesll]

I searched into it and the problem is indeed with the installation of the Python gcvspline package. It creates too much problem and is now removed from Rampy. I also considered using the Gcvspl Julia wrapper that I maintain, but again too much problem with compilation.

It turns out that DataInterpolations.jl maintains a GCV smoothing algorithm that is very similar. I am re-writting the baseline() function in pure Julia with using this method. This will be pushed with the next version.

[Matheus-gif]

I see, thank you very much for your replies. Funny enough, I was thinking of installing a Fortran compiler (suggested by chatgpt), but I was under the impression that wouldn't be a good idea, I'll be looking foward to the next version.

[charlesll]

@Matheus-gif v2.0.1 does not rely on the fortran GCVSPL code, we use the GCV spline from DataInterpolations.jl. Check the new code and docs, this is solved now!