Simplify digitizer functions and pulse ID coordinates assignment for XGM, digitizers

Involved: @lleguy @gortr @mercurio

The aim is to clarify/simplify the code for data extraction of point detectors (pulse-resolved data that produces one value per pulse, such as digitizer peaks, XGM, BAM values). The detectors should each have a simple function get_xgm(), get_bam(), get_tim_peaks(), etc, that extracts the relevant values and aligns the pulse ID according to the bunch pattern table. Eventually, these functions should be run in the load function.

The new features are:

• A new file digitizers.py, with one general function get_digitizers_peaks that can take any FastADC or ADQ412 data. For convenience, get_tim_peaks() and get_laser_peaks() are special calls to get_digitizers_peaks, tailored for SCS data. The peaks are loaded from peak-integrated values by the digitizer or automatically detected from raw traces and the bunchpattern is used to assign pulse ID.
• Possibility to get / visually inspect the peak-integration parameters of the digitizer parameters or the peak finding algorithm results with check_peaks_params
• The xgm.py functions are simplified to 3 functions: get_xgm(), align_xgm_array() and calibrate_xgm().
• A new file bam_detectors.py that extracts and aligns any BAM data.
• useage of the bunch_pattern_external module, with addition of function is_pulse_at()
• The load function is modified and returns both the extra_data DataCollection and the processed xarray Dataset.
• Documentation on the new features is started, some of it via a Jupyter notebook.

The consequences are:

• The sase1, sase3, npulses_sase1, npulses_sase3 arrays in the load function are not required and not loaded anymore.
• Instead, the bunchPatternTable is loaded by default, to speed up each of these new functions (currently they each load the bunch pattern table).
• The function extractBunchPattern, and, in general, the file bunch_pattern.py is not useful and could be removed.
• The functions that load TIM and XGM data in DSSC were adapted accordingly

src/toolbox_scs/detectors/__init__.py

+from .load_detectors import (
+    get_all_detectors)
 from .xgm import (
-    load_xgm, cleanXGMdata, matchXgmTimPulseId, calibrateXGMs,
+    load_xgm, get_xgm, cleanXGMdata, matchXgmTimPulseId, calibrateXGMs,
     autoFindFastAdcPeaks)
 from .tim import (
     load_TIM,)
+from .digitizers import (
+    get_peaks, get_tim_peaks, get_fast_adc_peaks, check_peak_params)
 from .dssc_data import (
     save_xarray, load_xarray, get_data_formatted, save_attributes_h5)
 from .dssc_misc import (
@@ -12,14 +16,21 @@ from .dssc_processing import (
     process_dssc_data)
 from .dssc import (
     DSSCBinner, DSSCFormatter)
-from .azimuthal_integrator import AzimuthalIntegrator, AzimuthalIntegratorDSSC
+from .azimuthal_integrator import (
+    AzimuthalIntegrator, AzimuthalIntegratorDSSC)
 
 __all__ = (
     # Functions
+    "get_all_detectors",
     "load_xgm",
+    "get_xgm",
     "cleanXGMdata",
     "load_TIM",
     "matchXgmTimPulseId",
+    "get_peaks",
+    "get_tim_peaks",
+    "get_fast_adc_peaks",
+    "check_peak_params",
     "load_dssc_info",
     "create_dssc_bins",
     "calc_xgm_frame_indices",
@@ -60,6 +71,8 @@ clean_ns = [
     'FastCCD',
     'tim',
     'xgm',
+    'digitizers',
+    'load_detectors'
     ]