.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/3_Fitting/plot1_fit_Tgas.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note You can download :ref:`below ` the full example code and run it with 🔬 `Radis-Lab `__, .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_3_Fitting_plot1_fit_Tgas.py: ================================================================================ Example #1: Temperature fit ================================================================================ RADIS has its own fitting feature, as shown in `1 temperature fit example `, where you have to manually create the spectrum model, input the experimental spectrum and other ground-truths into numerous RADIS native functions, and adjust the fitting pipeline yourself. Now with the new fitting module released, all you have to do is to prepare a .spec file containing your experimental spectrum, fill some JSON forms describing the ground-truth conditions just like how you fill a medical checkup paper, call the function :py:func:`~radis.tools.new_fitting.fit_spectrum` and let it do all the work! If you are not satisfied with the result, you can simply adjust the parameters in your JSON such as slit and path_length, recall the function until the results are good. Instruction: - Step 1: prepare a .spec file. Create a .spec file containing your experimental spectrum. You can do it with RADIS by saving a Spectrum object with :py:meth:`~radis.spectrum.spectrum.Spectrum.store`. If your current data is not a Spectrum object, you can convert it to a Spectrum object from Python arrays or from text files, and then save it as .spec file as above. - Step 2: fill the JSON forms. There are 4 JSON forms you need to fill: `experimental_conditions` with ground-truth data about your experimental environment, `fit_parameters` with the parameters you need to fit (such as Tgas, mole fraction, etc.), `bounding_ranges` with fitting ranges for parameters you listed in `fit_parameters`, and `fit_properties` for some fitting pipeline references. - Step 3: call :py:func:`~radis.tools.new_fitting.fit_spectrum` with the experimental spectrum and 4 JSON forms, then see the result. This example features fitting an experimental spectrum with Tgas, using new fitting modules. .. GENERATED FROM PYTHON SOURCE LINES 38-129 .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/3_Fitting/images/sphx_glr_plot1_fit_Tgas_001.png :alt: plot1 fit Tgas :srcset: /auto_examples/3_Fitting/images/sphx_glr_plot1_fit_Tgas_001.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/3_Fitting/images/sphx_glr_plot1_fit_Tgas_002.png :alt: plot1 fit Tgas :srcset: /auto_examples/3_Fitting/images/sphx_glr_plot1_fit_Tgas_002.png :class: sphx-glr-multi-img .. rst-class:: sphx-glr-script-out .. code-block:: none ======================= COMMENCE FITTING PROCESS ======================= Successfully retrieved the experimental data in 0.0028083324432373047s. Acquired spectral quantity 'radiance' from the spectrum. NaN values successfully purged.Number of data points left: 16666 points. Successfully refined the experimental data in 0.0011081695556640625s. /home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/db/molparam.py:252: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\s+'`` instead "tol" parameter spotted but "method" is not "lbfgsb"! 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[[Fit Statistics]] # fitting method = least_squares # function evals = 16 # data points = 1 # variables = 1 chi-square = 8.9285e-14 reduced chi-square = 8.9285e-14 Akaike info crit = -28.0469393 Bayesian info crit = -30.0469393 [[Variables]] Tgas: 1000.10724 +/- 100.024057 (10.00%) (init = 700) Successfully finished the fitting process in 4.478511571884155s. /home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/misc/curve.py:268: UserWarning: First spectrum has more resolution than 2nd. Reverse your spectra in interpolation/comparison for a better accuracy /home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/misc/curve.py:268: UserWarning: First spectrum has more resolution than 2nd. Reverse your spectra in interpolation/comparison for a better accuracy /home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/misc/curve.py:241: UserWarning: Presence of NaN in curve_divide! Think about interpolation=2 ======================== END OF FITTING PROCESS ======================== Residual history: [2.224477429034679e-05, 2.224477385113398e-05, 6.249578962391826e-06, 6.249580255421773e-06, 6.706460342392087e-07, 6.706471653673713e-07, 3.2846836157924164e-07, 3.284678382718015e-07, 7.09127746840601e-07, 3.042829847388958e-07, 3.0428322638140504e-07, 3.0905702837905567e-07, 2.995759883226966e-07, 2.9957608878233613e-07, 2.9880650099886707e-07, 2.9880645647916407e-07, 2.9880650099886707e-07] Fitted values history: [700.0] [700.0000104308128] [1075.638226979803] [1075.6382430080616] [1007.3582150545501] [1007.3582300653572] [998.6117334307623] [998.6117483112367] [1007.8655617530042] [1000.9251905113227] [1000.9252054262704] [999.288951911667] [1000.5161308614088] [1000.5161457702609] [1000.1072382663516] [1000.1072531691108] [1000.1072382663516] Total fitting time: 4.478511571884155 s | .. code-block:: Python import astropy.units as u from radis import load_spec from radis.test.utils import getTestFile from radis.tools.new_fitting import fit_spectrum # -------------------- Step 1. Load experimental spectrum -------------------- # # Load an experimental spectrum. You can prepare yours, or fetch one of them in the radis/test/files directory. my_spec = getTestFile("synth-NH3-1-500-2000cm-P10-mf0.01-p1.spec") s_experimental = load_spec(my_spec) # -------------------- Step 2. Fill ground-truths and data -------------------- # # Experimental conditions which will be used for spectrum modeling. Basically, these are known ground-truths. experimental_conditions = { "molecule": "NH3", # Molecule ID "isotope": "1", # Isotopologue - also "all" or "1,2" "wmin": 1000, # Starting wavelength/wavenumber to be cropped out from the original experimental spectrum. "wmax": 1050, # Ending wavelength/wavenumber for the cropping range. "wunit": "cm-1", # Unit of "wmin"/"wmax" "mole_fraction": 0.01, # Species mole fraction, from 0 to 1. "pressure": 1e6 * u.Pa, # Total pressure of gas, in "bar" unit by default, but you can also use Astropy units. "path_length": 10 * u.mm, # Experimental path length, in "cm" unit by default, but you can also use Astropy units. "slit": "1 nm", # Experimental slit, must be a blank space separating slit amount and unit. "offset": "-0.2 nm", # Experimental offset, must be a blank space separating offset amount and unit. "databank": "hitran", # Databank used for the spectrum calculation. Must be stated. } # List of parameters to be fitted, accompanied by their initial values. # Comment : an initial parameter too far from reality will impede convergence fit_parameters = { "Tgas": 700, # Gas temperature, in K. } # List of bounding ranges applied for those fit parameters above. # You can skip this step and let it use default bounding ranges, but this is not recommended. # Bounding range must be at format [, ]. bounding_ranges = { "Tgas": [500, 2000], } # Fitting pipeline setups. fit_properties = { "method": "least_squares", # Preferred fitting method from the 17 confirmed methods of LMFIT stated in week 4 blog. By default, "leastsq". "fit_var": "radiance", # Spectral quantity to be extracted for fitting process, such as "radiance", "absorbance", etc. "normalize": False, # Either applying normalization on both spectra or not. "max_loop": 150, # Max number of loops allowed. By default, 200. "tol": 1e-15, # Fitting tolerance, only applicable for "lbfgsb" method. } """ For the fitting method, you can try one among 17 different fitting methods and algorithms of LMFIT, introduced in `LMFIT method list `. You can see the benchmark result of these algorithms here: `RADIS Newfitting Algorithm Benchmark `. """ # -------------------- Step 3. Run the fitting and retrieve results -------------------- # # Conduct the fitting process! s_best, result, log = fit_spectrum( s_exp=s_experimental, # Experimental spectrum. fit_params=fit_parameters, # Fit parameters. bounds=bounding_ranges, # Bounding ranges for those fit parameters. model=experimental_conditions, # Experimental ground-truths conditions. pipeline=fit_properties, # Fitting pipeline references. fit_kws={"gtol": 1e-12}, ) # Now investigate the result logs for additional information about what's going on during the fitting process print("\nResidual history: \n") print(log["residual"]) print("\nFitted values history: \n") for fit_val in log["fit_vals"]: print(fit_val) print("\nTotal fitting time: ") print(log["time_fitting"], end=" s\n") .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 6.593 seconds) .. _sphx_glr_download_auto_examples_3_Fitting_plot1_fit_Tgas.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot1_fit_Tgas.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot1_fit_Tgas.py `