[AGIPD] [CORRECT] Fix / Correcting AGIPD run with no images.

Twp bugs were found when there was a request to correct AGIPD@MID runs with no data.

1. The printout for the empty modules was wrong Q4M4(AGIDP00).
2. The report was not created.

Traceback (most recent call last):
  File "/home/xcal/.pyenv/versions/3.8.11/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/xcal/.pyenv/versions/3.8.11/lib/python3.8/multiprocessing/pool.py", line 51, in starmapstar
    return list(itertools.starmap(args[0], args[1]))
  File "<ipython-input-9-2025cd48196c>", line 23, in retrieve_constants
    raise ValueError(
ValueError: No raw images found for Q4M4(AGIPD02) for all sequences

Description

• The wrong module_index was used for indexing modules when it comes to printing empty module or selecting slopes_ff local constants.
• Removed unused defined parameters.
• A pre-check if all modules have no images for an early exit.
• Making sure the notebook runs fine if one module has no images.
• Fill the summary table for constants successfully with a no constants retrieved text. To avoid latex errors while creating the report.

How Has This Been Tested?

• Interactively, by running the notebook.

• Running automated test.

Relevant Documents (optional)

• Attach a report for an empty AGIPD MID run.

no_images_agipd_mid_report.pdf

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Checklist:

Reviewers

@calibration

notebooks/AGIPD/AGIPD_Correct_and_Verify_Summary_NBC.ipynb

 %% Cell type:markdown id: tags:
 
 # Summary of the AGIPD offline correction #
 
 %% Cell type:code id: tags:
 
 ``` python
 run = 11 # runs to process, required
 out_folder = "/gpfs/exfel/data/scratch/ahmedk/test/AGIPD_Corr" # path to output to, required
 karabo_id = "SPB_DET_AGIPD1M-1" # karabo karabo_id
 modules = [-1]
 karabo_da = ['-1']  # a list of data aggregators names, Default [-1] for selecting all data aggregators
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 import re
 import warnings
 from pathlib import Path
 
 import dateutil.parser
 import numpy as np
 import yaml
 
 warnings.filterwarnings('ignore')
 
 import matplotlib.pyplot as plt
 
 %matplotlib inline
 import tabulate
 from cal_tools.tools import CalibrationMetadata
 from IPython.display import Latex, Markdown, display
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 out_folder = Path(out_folder)
 metadata = CalibrationMetadata(out_folder)
 const_dict = metadata.setdefault("retrieved-constants", {})
 time_dict = const_dict.setdefault("time-summary", {})
 
 # Extracting Instrument string
 instrument = karabo_id.split("_")[0]
 # Evaluate detector instance for mapping
 if instrument == "SPB":
     dinstance = "AGIPD1M1"
     nmods = 16
 elif instrument == "MID":
     dinstance = "AGIPD1M2"
     nmods = 16
 elif instrument == "HED":
     dinstance = "AGIPD500K"
     nmods = 8
 
 if karabo_da[0] == '-1':
     if modules[0] == -1:
         modules = list(range(nmods))
     karabo_da = ["AGIPD{:02d}".format(i) for i in modules]
 else:
     modules = [int(x[-2:]) for x in karabo_da]
 
 # This is needed only if AGIPD Correction notebook had no precorrection notebooks for retrieving constants
 # gather all generated sequence yml files for time summary of retrieved constant under retrieved-constants in metadata.yml
 for fn in sorted(out_folder.glob("retrieved_constants_*.yml")):
     with fn.open("r") as fd:
         fdict = yaml.safe_load(fd)
     # append different sequences' time summary to the main yaml
     time_dict.update(fdict["time-summary"])
     fn.unlink()
 
 metadata.save()
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 def print_const_table(const):
     print(f"{const} constants were injected on:")
     table_data = {}
     for seq, mod_data in time_dict.items():
         for mod, const_data in mod_data.items():
             timestamp = const_data[const]
             table_data.setdefault(timestamp, []).append(f"{seq}:{mod}")
     table = []
-    if len(table_data) == 1:
+    if not len(table_data):
+        table.append(["No constants retrieved"])
+    elif len(table_data) == 1:
         table.append([[*table_data][0], "All modules"])
     else:
         for timestamp, seqmod in table_data.items():
             table.append([timestamp, seqmod[0]])
             for further_module in seqmod[1:]:
                 table.append(["", further_module])
     display(Latex(tabulate.tabulate(table,
                  tablefmt="latex",
                  headers=["Timestamps", "Modules and sequences"])))
 
 for const in ['Offset', 'SlopesPC', 'SlopesFF']:
     print_const_table(const)
 ```
 
-%% Cell type:code id: tags:
 
-``` python
 ```

[Karim Ahmed]

This part prevented the report to be created with a latex bug.

Chapter 3.
(/software/opt/texlive/2019/texmf-dist/tex/latex/psnfss/t1pcr.fd)

! Package array Error: Empty preamble: `l' used.

See the array package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.196 \end{tabular}\end{split}
                              
? 
! Emergency stop.
 ...                                              
                                                  
l.196 \end{tabular}\end{split}
                              
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on AGIPDOfflineCorrection.log.
Latexmk: Index file 'AGIPDOfflineCorrection.idx' was written
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
=== TeX engine is 'pdfTeX'