vosjo / speedyfit

Python package to fit single and binary photometric SEDs. Automatically pull archive photometry from the main surveys and use Bayesian inference to derive atmospheric parameters.

Hi there 👋

I am a scientist with an education in Astrophysics. I am an end-to-end data scientist and worked on projects covering the entire path from problem definition, data acquisition, data reduction and cleaning, hypothesis testing, model creation and testing, and reporting on the results. Below you can find a few python packages for the aquisition and modeling of astronomical data that I have developed during my career in astronomy.

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speedyfit's Issues

grid_description.yaml file not found

Hi, when I run "speedyfit checkgrids", it shows:

grid_description.yaml file not found or no models included in the description file.
Please add a grid_description.yaml file in the SPEEDYFIT_MODELS directory

So how to make the grid_description.yaml file? What's the format of the file? Thanks!

How to set up to use more photometry sources

Hi Joris,

I want to use more photometry sources. Should I how to set that up?

Thanks!

Poor handling of path specified by SPEEDYFIT_MODELS environment variable

It is unclear from the installation instructions that the environment variable SPEEDYFIT_MODELS must include the trailing "/" or ""

Rather than fixing the documentation, it would be better to use os.path.join in the code to join filenames and paths correctly without the user needing to worry about trailing slashes, etc.

Citation

Hi Joris, this is a great package and I've used it to model one of my systems (which agrees well with results I obtained independently). Would you consider packaging it to Zenodo or something similar so it can be cited in our paper?

Thanks!

How to add a BB model within speedyfit?

Hi,

How to an extra model of blackbody within SED using the speedyfit?

Thanks!

Grid name (kurucz) not recognized!

I want to use the kurucz grid to plot my SED directly. However, when I use the function named get_table_single() with grid='kurucz', there is an error raised. It shows that grid name (Kurucz) not recognized!. I want to know how to call the kurucz grid.

grid_description.yaml file not found

I have grid_description.yaml in the corresponding directory, but after executing ''speedyfit checkgrids'', python told me that there is no grid_description.yaml file

’‘‘
Checking which atmosphere models are available...
Checking for models in </home/ymk/miniconda3/sed_models to extracted atmosphere models>
grid_description.yaml file not found or no models included in the description file.
Please add a grid_description.yaml file in the SPEEDYFIT_MODELS directory.
’’’

My directory contains the following files:
blackbody_discint.fits
grid_description.yaml
iblackbody_discint_lawfitzpatrick2004_Rv3.10.fits
ikurucz93_z0.0_k2odfnew_sed_lawfitzpatrick2004_Rv3.10.fits
iMunari2005_extended_lawfitzpatrick2004_Rv3.10.fits
iTMAP2012_sdOB_extended_lawfitzpatrick2004_Rv3.10.fits
kurucz93_z0.0_k2odfnew_sed.fits
Munari2005_extended.fits
TMAP2012_sdOB_extended.fits

The grid_description.yaml is just in directory. I do not know how to solve it. Please.

Thanks very much.

extending the grids?

Hi Joris,
Really nice code! The integrated grids you include are, however, quite limited in extinction, would it be possible to extend that to (much) larger values? Probably you have all the required steps already...

Install and download photometry

Hi Joris,

I use speedyfit checkgrids to check whether everything went well after I install speedyfit. However, an error is given, which is not the problem of SPEEDYFIT_MODELS environmental variable. This error is as follow:

In addition, I use command (speedyfit phot J183656.3+384701.2) to obtain the data of J183656.3+384701.2. Here, anther error is given, which is as follow:

I don't know what caused those problem. Could you give me some suggestions?

Thanks!

grid_description.yaml missing from modelgrids.tar.gz (?)

I have followed the installation instructions at https://speedyfit.readthedocs.io/en/stable/userguide/install.html

I get the following error.

$ speedyfit checkgrids 
Checking which atmosphere models are available... 
Checking for models in /home/jovyan/modelgrids 
grid_description.yaml file not found or no models included in the description file. 
Please add a grid_description.yaml file in the SPEEDYFIT_MODELS directory.

Should the file grid_description.yaml be included with modelgrids.tar.gz?

ValueError: shape mismatch in running the fit

Thank you for the really helpful and nicely accessible package. I have been trying to run example cases (e.g., HIP 4618, or something else well observed and bright, e.g., Cyg X-1). The setup step (speedyfit setup "Cyg_X-1" -grid kurucz --phot) goes well and finds relevant measurements, etc. However, the fitting step fails:

speedyfit fit Cyg_X-1_setup_kurucz.yaml
.
.
.
  File "speedyfit/interpol.py", line 79, in create_pixeltypegrid
    pixelgrid[indices] = grid_data.T
ValueError: shape mismatch: value array of shape (615,19) could not be broadcast to indexing result of shape (3,615,8,3,19)

I'm running Speedyfit 0.2.3 (installed through pip) and Numpy 1.23.5 on Python 3.10.8.

Thanks for your help.

"No models were accepted" issue

Hi @vosjo,

I get this error when I run your code for HIP 4648. Can you help me?