[PNCCD][DARK][CORRECT] Fix pnccd notebooks after pre release test. 3.5.0b1

While testing tag: 3.5.0a2 it was realized that as we don't use try/except the notebook fails if slow data is not available.

Description

• I removed a flag I created in the past changes set_parameters_manually it add more unneed configs. and one should set fix_temperature_bot the same as fix_temperature_top in the calibration_configurations to avoid job failures for processing old data.
• Process all trains for dark processing by setting max_trains = 0
• Keep Offset constant dtype = float64 like before.
• copy raw image back like before until further discussion.

How Has This Been Tested?

Tested again with proposal 900113 run 9989 along with the other changes in latest beta tag 3.5.0b1

Relevant Documents (optional)

Types of changes

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

Checklist:

Reviewers

@calibration