Possible Bug In `fit_spectrum` Which Is Causing Value Error
Introduction
The fit_spectrum function in the Radis library is used to refine experimental data by fitting a model to it. However, in some cases, this function throws a Value Error. In this article, we will investigate the possible cause of this error and provide a solution.
Background
Radis is a Python library for radiative transfer calculations. It provides a range of tools for simulating and analyzing spectra. The fit_spectrum function is a key part of this library, allowing users to refine their experimental data by fitting a model to it.
The Error
The error occurs when the fit_spectrum function is called with certain parameters. The error message is as follows:
ValueError: radiance_noslit not in Spectrum arrays ['radiance']. An error occurred while trying to recompute it from the available arrays and conditions. See above
Investigation
To investigate this error, we need to look at the code that calls the fit_spectrum function. The code is as follows:
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.
)
Possible Cause
The error occurs because the fit_spectrum function is trying to retrieve the radiance_noslit value from the Spectrum object, but it is not available. This is because the radiance_noslit value is not calculated by the fit_spectrum function.
Solution
To solve this error, we need to modify the fit_spectrum function to calculate the radiance_noslit value before trying to retrieve it. We can do this by adding the following line of code to the fit_spectrum function:
self.update("radiance_noslit", verbose=False)
This will calculate the radiance_noslit value and make it available for retrieval.
Conclusion
In conclusion, the error in the fit_spectrum function is caused by the function trying to retrieve the radiance_noslit value without calculating it first. By adding a line of code to calculate the radiance_noslit value, we can solve this error and ensure that the fit_spectrum function works correctly.
Code Changes
The following code changes are required to solve this error:
def fit_spectrum(self, s_exp, fit_params, model, pipeline, bounds, input_file, verbose, show_plot, fit_kws):
# ...
self.update("radiance_noslit", verbose=False)
# ...
Commit Message
The following commit message can be used to commit the code changes:
Fixed error in fit_spectrum function by calculating radiance_noslit value
API Documentation
The following API documentation can be used to document the fit_spectrum function:
def fit_spectrum(self, s_exp, fit_params, model, pipeline, bounds, input_file, verbose, show_plot, fit_kws):
"""
Refine experimental data by fitting a model to it.
Parameters:
s_exp (Spectrum): Experimental spectrum.
fit_params (dict): Fit parameters.
model (dict): Experimental ground-truths conditions.
pipeline (dict): Fitting pipeline references.
bounds (dict): Bounding ranges for fit parameters.
input_file (str): Input file.
verbose (bool): Verbose mode.
show_plot (bool): Show plot.
fit_kws (dict): Additional keyword arguments.
Returns:
tuple: Best fit spectrum, result, and log.
"""
Testing
The following test can be used to test the fit_spectrum function:
import unittest
from radis import Spectrum
class TestFitSpectrum(unittest.TestCase):
def test_fit_spectrum(self):
# Create a Spectrum object
s = Spectrum()
# Define experimental spectrum
s_exp = Spectrum()
# Define fit parameters
fit_params = {"param1": 1, "param2": 2}
# Define experimental ground-truths conditions
model = {"condition1": 1, "condition2": 2}
# Define fitting pipeline references
pipeline = {"reference1": 1, "reference2": 2}
# Define bounding ranges for fit parameters
bounds = {"param1": (1, 10), "param2": (1, 10)}
# Define input file
input_file = "input_file.txt"
# Define verbose mode
verbose = True
# Define show plot
show_plot = True
# Define additional keyword arguments
fit_kws = {"kwarg1": 1, "kwarg2": 2}
# Call fit_spectrum function
s_best, result, log = fit_spectrum(s_exp, fit_params, model, pipeline, bounds, input_file, verbose, show_plot, fit_kws)
# Assert that the function returns the expected values
self.assertEqual(s_best, "best fit spectrum")
self.assertEqual(result, "fit result")
self.assertEqual(log, "fit log")
```<br/>
**Q&A: Possible Bug in `fit_spectrum` Causing Value Error**
=====================================================
**Q: What is the possible bug in `fit_spectrum` causing a Value Error?**
----------------------------------------------------------------
A: The possible bug in `fit_spectrum` causing a Value Error is that the function is trying to retrieve the `radiance_noslit` value from the Spectrum object without calculating it first.
**Q: What is the error message when the `fit_spectrum` function is called?**
-------------------------------------------------------------------
A: The error message when the `fit_spectrum` function is called is:
ValueError: radiance_noslit not in Spectrum arrays ['radiance']. An error occurred while trying to recompute it from the available arrays and conditions. See above
**Q: What is the cause of the error?**
-----------------------------------
A: The cause of the error is that the `fit_spectrum` function is trying to retrieve the `radiance_noslit` value without calculating it first.
**Q: How can the error be solved?**
-----------------------------------
A: The error can be solved by adding a line of code to the `fit_spectrum` function to calculate the `radiance_noslit` value before trying to retrieve it.
**Q: What is the code change required to solve the error?**
---------------------------------------------------
A: The code change required to solve the error is to add the following line of code to the `fit_spectrum` function:
```python
self.update("radiance_noslit", verbose=False)
Q: What is the commit message for the code change?
A: The commit message for the code change is:
Fixed error in fit_spectrum function by calculating radiance_noslit value
Q: What is the API documentation for the fit_spectrum function?
A: The API documentation for the fit_spectrum function is:
def fit_spectrum(self, s_exp, fit_params, model, pipeline, bounds, input_file, verbose, show_plot, fit_kws):
"""
Refine experimental data by fitting a model to it.
Parameters:
s_exp (Spectrum): Experimental spectrum.
fit_params (dict): Fit parameters.
model (dict): Experimental ground-truths conditions.
pipeline (dict): Fitting pipeline references.
bounds (dict): Bounding ranges for fit parameters.
input_file (str): Input file.
verbose (bool): Verbose mode.
show_plot (bool): Show plot.
fit_kws (dict): Additional keyword arguments.
Returns:
tuple: Best fit spectrum, result, and log.
"""
Q: What is the test for the fit_spectrum function?
A: The test for the fit_spectrum function is:
import unittest
from radis import Spectrum
class TestFitSpectrum(unittest.TestCase):
def test_fit_spectrum(self):
# Create a Spectrum object
s = Spectrum()
# Define experimental spectrum
s_exp = Spectrum()
# Define fit parameters
fit_params = {"param1": 1, "param2": 2}
# Define experimental ground-truths conditions
model = {"condition1": 1, "condition2": 2}
# Define fitting pipeline references
pipeline = {"reference1": 1, "reference2": 2}
# Define bounding ranges for fit parameters
bounds = {"param1": (1, 10), "param2": (1, 10)}
# Define input file
input_file = "input_file.txt"
# Define verbose mode
verbose = True
# Define show plot
show_plot = True
# Define additional keyword arguments
fit_kws = {"kwarg1": 1, "kwarg2": 2}
# Call fit_spectrum function
s_best, result, log = fit_spectrum(s_exp, fit_params, model, pipeline, bounds, input_file, verbose, show_plot, fit_kws)
# Assert that the function returns the expected values
self.assertEqual(s_best, "best fit spectrum")
self.assertEqual(result, "fit result")
self.assertEqual(log, "fit log")
Q: What is the solution to the error?
A: The solution to the error is to add a line of code to the fit_spectrum function to calculate the radiance_noslit value before trying to retrieve it.