Improving flux fitting by using different mask

[andrea-pasquale]

In this PR I'm trying to improve the performance of the fit by doing the following:

1. Adding more parameters (in this way we avoid to rely on outdated parameters from the JSON files) + using a slight different formula
2. Instead of using a mask based on the confidence interval I'm using a different approach where after averaging the signal for each column (which should compensate any unwanted noise) I'm just calculating the peaks using find_peaks with a suitable prominence.

Here is how the fitting are looking now: http://login.qrccluster.com:9000/f4DP80QOStCzwaBP2XQxAQ==/
Compared to before where the fitting was failing: http://login.qrccluster.com:9000/x9YShaUsRU6rRJRAnmRd1w==/

I've also decided to remove the information related to the phase since it is not relevant for the fit. If we can confirm this I can refactor also the acquisition to simplify it removing the phase.

[codecov]

Codecov Report

❌ Patch coverage is 98.70130% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 97.81%. Comparing base (dbdeaa0) to head (a5a7c5f).
⚠️ Report is 14 commits behind head on main.

Files with missing lines	Patch %	Lines
...ocols/flux_dependence/resonator_flux_dependence.py	90.90%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1229   +/-   ##
=======================================
  Coverage   97.81%   97.81%           
=======================================
  Files         132      132           
  Lines       10039    10041    +2     
=======================================
+ Hits         9820     9822    +2     
  Misses        219      219           

Flag	Coverage Δ
unittests	97.81% <98.70%> (+<0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
...bocal/protocols/flux_dependence/qubit_crosstalk.py	98.43% <100.00%> (-0.03%)	⬇️
...protocols/flux_dependence/qubit_flux_dependence.py	98.26% <100.00%> (-0.02%)	⬇️
src/qibocal/protocols/flux_dependence/utils.py	100.00% <100.00%> (+1.61%)	⬆️
...s/qubit_spectroscopies/qubit_power_spectroscopy.py	100.00% <100.00%> (ø)
...ols/resonator_spectroscopies/resonator_punchout.py	100.00% <100.00%> (ø)
src/qibocal/protocols/utils.py	91.90% <100.00%> (+0.43%)	⬆️
...ocols/flux_dependence/resonator_flux_dependence.py	98.24% <90.90%> (-0.15%)	⬇️

... and 1 file with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

[andrea-pasquale]

I took the opportunity to refactor and modify slightly the plots. Here are two examples

[alecandido]

Defining these at the beginning of the function, you could use them even in the reshape.

[lballerio]

same as lines 143-144-145, remove for redundancy?

[lballerio]

typo in the comment: correct:

"""Custom dtype for qubit flux dependence."""

[alecandido]

Suggested change

	"""Custom dtype for resonator flux dependence."""
	"""Custom dtype for qubit flux dependence."""

[lballerio]

All changes in protocols are minor changes, mainly the elaboration of phase data of the measured signal is deleted, and only the magnitude is processed.
Parent class FluxFrequencySweepParameters is defined as a parent class for all single protocols, but in general all the input parameters are maintained for each protocol.

This branch was tested with qubit_flux experiment, when a problem in extract_feature arose for pathological cases for qubit_flux experiment: before merging to main see stabilize-extract-feature branch for stabilizing extract_feature