[Generic][Shimadzu] Dynamic flat-field characterization and correction for MHz microscopy

This implements:

1. The characterization of dark and flat fields of Shimadzu HPVX2 images
2. The correction for Shimadzu HPVX2 images by applying offsets subtraction and dynamic flat-field correction.

Depends on the https://github.com/sarlotabirnsteinova/OnlineVisualization

This is needed for MHz microscopy at SPB

Features:

• Split on sequence files by 200 trains, ignoring original splitting
• Creates new source name SPB_EHD_MIC/CAM/HPVX2_1:daqOutput -> SPB_EHD_MIC/CORR/HPVX2_1:output

Corrected files structure

CORR-R0003-HPVX01-S00000.h5 ├INDEX │ ├SPB_EHD_MIC │ │ └CORR │ │ ├HPVX2_1:output │ │ │ └index_group │ │ │ ├count [uint64: 15] │ │ │ └first [uint64: 15] │ │ └HPVX2_2:output │ │ └index_group │ │ ├count [uint64: 15] │ │ └first [uint64: 15] │ ├flag [int32: 15] │ ├origin [int32: 15] │ ├timestamp [uint64: 15] │ └trainId [uint64: 15] ├INSTRUMENT │ └SPB_EHD_MIC │ └CORR │ ├HPVX2_1:output │ │ └data │ │ └image │ │ ├binning [uint64: 9 × 3] │ │ ├dimTypes [int32: 9 × 3] │ │ ├dims [uint64: 9 × 3] │ │ ├flipX [uint8: 9] │ │ ├flipY [uint8: 9] │ │ ├pixels [float32: 9 × 128 × 250 × 400] │ │ ├roiOffsets [uint64: 9 × 3] │ │ └rotation [int32: 9] │ └HPVX2_2:output │ └data │ └image │ ├binning [uint64: 10 × 3] │ ├dimTypes [int32: 10 × 3] │ ├dims [uint64: 10 × 3] │ ├flipX [uint8: 10] │ ├flipY [uint8: 10] │ ├pixels [float32: 10 × 128 × 250 × 400] │ ├roiOffsets [uint64: 10 × 3] │ └rotation [int32: 10] └METADATA ├creationDate [ASCII string: 1] ├daqLibrary [ASCII string: 1] ├dataFormatVersion [ASCII string: 1] ├dataSources │ ├dataSourceId [ASCII string: 2] │ ├deviceId [ASCII string: 2] │ └root [ASCII string: 2] ├karaboFramework [ASCII string: 1] ├proposalNumber [uint32: 1] ├runNumber [uint32: 1] ├sequenceNumber [uint32: 1] └updateDate [ASCII string: 1]

Reports:

• characterization report: dark_runs_1_2_v0.pdf
• correction report: r0003.pdf

cc @schmidtp

docs/operation/calibration_database.md

@@ -103,7 +103,8 @@ constants files)
 
 PDUs can be transferred between detectors and instruments or replaced. To correct raw data, the calibration pipeline produces calibration constants, which are specific to the module they were generated from. As a result, it's crucial to map the hardware to the corresponding software modules.
 
-As the detector is 
+It's possible to update a detector mapping through CalCat in case the PDUs are already available. i.e. moving a PDU from one detector to another. Otherwise, only users with admin access can add entirely new PDUs.
+![detector_pdu_mapping_calcat](../static/calcat/detector_mapping_edit.png)
 
 
 ### Modifying detector mapping