How to add absorption to the model and set upper and lower limits

[unknowner-m]

I am a graduate student and I am trying to fit the NIRSPEC g395h spectrum using PAHFIT. According to Lai+2020, I added the short wavelength feature in the yaml file.

PAH_3.3:
  kind: dust_feature
  wavelength: 3.29
  fwhm: 0.0418

PAH_3.4:
  kind: dust_feature
  wavelength: 3.4
  fwhm: 0.0299

PAH_3.47:
  kind: dust_feature
  wavelength: 3.47
  fwhm: 0.1
##########################
# Absorption Model      #
##########################
H2O_absorption:
  kind: absorption
  tau: 2.5
  wavelength: 3.05
  fwhm: 0.406

CO2_absorption:
  kind: absorption
  tau: 1.532
  wavelength: 4.27
  fwhm: 0.033

CO_absorption:
  kind: absorption
  tau: 0.4
  wavelength: 4.67
  fwhm: 0.1

When I start running the script

model = Model.from_yaml('model.yaml')
model.guess(spec)
model.fit(spec, maxiter=10000)
display(model)
model.plot(spec)

I got the following error

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
Cell In[67], [line 12](vscode-notebook-cell:?execution_count=67&line=12)
     [10](vscode-notebook-cell:?execution_count=67&line=10) model.fit(spec, maxiter=10000)
     [11](vscode-notebook-cell:?execution_count=67&line=11) display(model)
---> [12](vscode-notebook-cell:?execution_count=67&line=12) model.plot(spec)

File d:\Anaconda\envs\pahfit\Lib\site-packages\pahfit\model.py:538, in Model.plot(self, spec, redshift, use_instrument_fwhm, label_lines, scalefac_resid, **errorbar_kwargs)
    [535] ext_model = S07_attenuation(tau_sil=tau)(lam_mod)
    [537](file:///D:/Anaconda/envs/pahfit/Lib/site-packages/pahfit/model.py:537) if has_abs:
--> [538](file:///D:/Anaconda/envs/pahfit/Lib/site-packages/pahfit/model.py:538)     raise NotImplementedError(
    [539](file:///D:/Anaconda/envs/pahfit/Lib/site-packages/pahfit/model.py:539)         "plotting absorption features not implemented yet"
    [540](file:///D:/Anaconda/envs/pahfit/Lib/site-packages/pahfit/model.py:540)     )
    [542](file:///D:/Anaconda/envs/pahfit/Lib/site-packages/pahfit/model.py:542) if has_att or has_abs:
    [543](file:///D:/Anaconda/envs/pahfit/Lib/site-packages/pahfit/model.py:543)     ax_att = ax.twinx()  # axis for plotting the extinction curve

NotImplementedError: plotting absorption features not implemented yet

Does this mean that the absorption feature cannot be applied in the current version?

In addition, I checked the feature table and found that the wavelength and fwhm of the features I added did not have upper and lower limits set. How should I set them correctly?

[drvdputt]

The fitting of the absorption features should be working normally. What you're seeing is just a plotting issue.

The error you posted is old code. The current plotting code definitely has something else under if has_abs.
Recently a lot of development in the dev branch was merged into master, but no official release was made.

Can you try installing the master branch? You can use pip install git+https://github.com/drvdputt/pahfit.git

[unknowner-m]

The fitting of the absorption features should be working normally. What you're seeing is just a plotting issue.

The error you posted is old code. The current plotting code definitely has something else under if has_abs. Recently a lot of development in the dev branch was merged into master, but no official release was made.

Can you try installing the master branch? You can use pip install git+https://github.com/drvdputt/pahfit.git

Thanks for your comment! I reinstalled PAHFIT using pip install git+https://github.com/drvdputt/pahfit.git but still got the same problem.

Then I checked out the other branch and installed it again using pip install git+https://github.com/PAHFIT/pahfit.git@dev, and now the code works perfectly.

However, I noticed that some checks for this branch were unsuccessful, as indicated on the github page, so perhaps this branch is temporarily unavailable?

[drvdputt]

Which checks are you referring to? I am not a aware of any particular problems.

[unknowner-m]

Which checks are you referring to? I am not a aware of any particular problems.

I am referring to the red crosses shown on the https://github.com/PAHFIT/pahfit/tree/dev page. Since I am a beginner, I don't know what this symbol means, but I guess it doesn't matter and the code works fine.

[drvdputt]

Thanks for bringing this up, it looks like one of the tests was not adapted to a recent format change of the Features table, and is therefore failing. Should be a quick fix in the testing code.

So this does not mean that anything is wrong, and since I am actively using the dev branch for my research (+ my changes committed on top of it), I assume it should also work for you.

[unknowner-m]

Thanks for bringing this up, it looks like one of the tests was not adapted to a recent format change of the Features table, and is therefore failing. Should be a quick fix in the testing code.

So this does not mean that anything is wrong, and since I am actively using the dev branch for my research (+ my changes committed on top of it), I assume it should also work for you.

Thank you for your answer！