Refactoring of the calibration and container module (#78)

* update SPE fit parameters initialization
* following updates of the ctapipe extractors
* improve the limits of generated charge histogram plots
* test script
* add method to sort WaveformsContainer and ChargesContainer following events_id
* waveformContainer contructor from event list
* user script for test ggroller
* change values of pp and n in fit parameters file by median
* improve test
* reduce pvalue digit in label
* add time counter to SPE fit
* add possibility to freeze parameters into minuit
* redesign of the SPE fit class to speed up
* new skeleton for the calibration pipeline :
  -container module for the data structure (to be extend)
  -makers module to make the computation of calibration quantities on the data structure
* mothers class for the maker module
* mother class for the gain makers
* FlatFieldSPEMaker implementation
* photostatistic maker (not re-implemented yet)
* implementation of the FFSPE fit for single run with n and p' fixed
* implementation of FF SPE gain maker at nominal voltage
* update of user script
* bugfix
user script updated : FF SPE at VVH voltage (ie for single run)

* update for nominal voltage data FF SPE fit from HHV
pre-computed one

* -bugfix
update for nominal FF SPE fit

* put I/O method in mother class

* add low gain in contructor (only high gain before)

* typo bugfiox

* move gain utils in one single folder

* bugfix nominal voltage fit
the fitting process continues although the initial
 parameters computation failed

* Photostatistic implementation done

* cleaning : import, type, etc

* remove old SPE fit implementation

* makers : core module enhancement
 (docstrings, unit test)

* cleaning

* moving container and makers in
 top of calibration directory

* folder restructuring

* cleaning after the restructuration

* unit test for chargecontainer

* test extractor utlis

* unit test CalibrationMaker and GainMakers

* unit test flatfieldSPEMakers

* unit test implementation follow up

* mv wavefomrs in makers

* code into WavefomContainers split into 2 parts : one for the data format,
the other for the computation

* move charge container into makers module

* creation of mother class to charge and waveform container

* follow up : factorisation waveforms and chargs Makers

* display module

* finalisation of the refactorisation of the waveformsMaker
chargesMaker implementation

* ChargesContainers I/O
cleaning
unit test for WaveformsMaker and ChargesMaker

* update calibration class following COntainers changes

* bugfix according to unit tests

* docstrings container + unit test

* make container module visible

* small bugfix + fix unit test for makers

* docstrings makers module

* follow pre-commit hook

* set Dirac import into methods which need it

* first step to reimplement following ctapipe
 Tool and Components framework

* -removed the I/O method for containers
    -> now we will use ctapipe HDF5TableWriter and Reader
-creation of recursive containers

* -adapt charges extraction makers and waveform extraction
makers with the ctapipe.Tool framework

* -creation of the component module, which inherits from ctapipe.component
-implementation of the NectarCAMComponent, the base class for nectrachain components,
- implementation of the ChargesComponent and WaveformsComponent

* -preliminary tuto script to extract charges
or waveforms using Tool and Component classes

---------

Co-authored-by: guillaume.grolleron <[email protected]>

src/nectarchain/calibration/README.md → src/nectarchain/README.md

@@ -1,7 +1,7 @@
 Environment variable needed: 
 export NECTARCAMDATA="path to local NectarCam data, it can contain fits.fz run files, WaveformsContainer or ChargeContainer FITS files"
 
-Environment variables which can be defined: 
+Environment variables which can be defined but are optional: 
 export NECTARCHAIN_TEST="path to test for nectarchain"
 export NECTARCHAIN_LOG="path to log for nectarchain"
 export NECTARCHAIN_FIGURES="path to log figures for nectarchain"

src/nectarchain/__init__.py

@@ -1,3 +1,3 @@
 from .version import __version__
 
-__all__ = ['__version__']
+__all__ = ["__version__"]