Major development of the various modules + many bugs were solved

See merge request cribe001/dlc_flytracker!10

Added intrinsic_from_extrinsic_and_coordinates and extrinsic_from_intrinsic_and_coordinates in camera.calib
+ renamed coords to coord when referring to a single set of 3d coordinates [x, y, z]

Made nb_dim a optional input for estim_dlt_coef

+ added example _full.pickle
+ removed Jupyter notebooks

+ Add main() in test functions
+ Changed res_method to fit_method

+ Merged camera.py and virtual_camera.py into objects.py

Wrote a test function test_calib_multi_focus to test calibration of one camera for multiple focus distances and focal lentghs

Added estimMDLT to estimate modified DLT coefficient (higher accuracy and orthogonal matrix -> needed to estimate quat)
+ Various changes to calib.py and debugging of related test functions

+ Modified settings to match recordings
+ Added sorting of frame numbers in ImageSequence class
+ Corrected back get_rotation_angle_btw_vectors
+ Some correction of docstrings

+ remove TODOs about using [0., 0., 1.] instead of [1., 0., 0.], was not necessary

+ Minor edits

+ Updated printed message during analysis
+ Changed folder tree + renamed some parameters files
+ Minor edits in Readme.md

Add correction factor to convert units of 3d coordinates use for the calibration (eg millimeters to meters)

+ Added functions to update .yaml with wing (skeleton/geometry) 3d coordinates from a .csv file that contains 2d coordinates

Minor edits (TODOs, docstrings, renaming variables, ...) and some minor debugging (dealing with nans, ...)

- DLT coefficient to/from intrinsic and extrinsic camera parameters (pinhole model)
- Improve modeling of 3d object, camera, mirror on a gimbal, and virtual camera
- test rotation matrices and pinhole camera model

+ Changed convention for normal vector of non-rotated object (from [1, 0, 0] to [0, 0, 1])
+ Use extrinsic rotation 'xyz' instead of intrinsic 'ZYX' for scipy.transform.Rotation
+ Implemented quaternions for calibration, Object3D, Camer, etc. But still need to implement them in skeleton_fitter
+ Improve documentation (doctstrings)

+ Other minor changes

Moved VirtualCamera(s) classes in their own .py + Various changes to VirtualCamera to prevent problems (e.g. it's not possible to set X,Y,Z and alpha,beta,gamma)

+Small changes to README.md

Worked on camera classes to handle 3d object(s), (virtual and real) camera(s) and mirror(s). (Work in progress)
+ Moved all virtual camera classes to cameras.py

Added functions to compute dlt coefficients from and to intrinsinc/extrincic parameters. (Work in progress)
Added camera classes to handle 3d object(s), (virtual and real) camera(s) and mirror(s). (Work in progress)
+ Moved example calibration files
+ Minor changes in README.md

All settings can now be read from a unique yaml file that contains settings for the batch processing and the protocol (e.g. all process steps)

Bug fixes for the various test functions

See merge request cribe001/dlc_flytracker!9

- Updated import calib in reconstructor3d.py
- Updated dlc_cfg_path to '/home/acribellier/Desktop/Antoine/_maDLC/config.yaml'
- Corrected docstrings

- Updated config.yaml
- Updated dlc_cfg_path to '../data/examples/mosquito_escapes/config.yaml'
- Corrected function name (convert_kwargs_to_be_writen_in_yaml > convert_kwargs_to_yaml)

# Conflicts:
#	point_tracker/reconstructor3d.py
#	process/batch_processing.py
#	process/dlc_postprocessing.py
#	process/utils.py
#	skeleton_fitter/animals/fly.py
#	skeleton_fitter/animals/fly_geo.py
#	skeleton_fitter/animals/fly_hybrid.py
#	skeleton_fitter/modules/bodies/insect_body_slim.py
#	skeleton_fitter/modules/limbs/insect_wings_flat.py
#	skeleton_fitter/skeleton_modules/insect_wings_flat_geo.py