Update S3 Ingestion workflow to support Alignment

[manasaV3]

Update the existing ingestion workflow to support capturing the new relevant metadata and updating the data structure as required.

The changes required for the entities are as follows:

Alignment

• Update the location of where alignment files are stored *.(xf|tlt|json|tltx|com)
• Update the files to have names such that <alignment-id>-<name-in-source>.<ext>
• Generate the alignment_metadata.json with the following metadata, handling cases where there are no alignment files are defined.

Field name	data type	source	default	computation logic if any
alignment_type	string	config metadata	GLOBAL
volume_dimension	dict
volume_dimension.(x,y,z)	int	related tomogram	-	if tomogram mrc, get nx,ny,nz from header / if tomogram zarr, get scale of 0 bin, The value should be multiplied with the voxel spacing to get the result in angstrom.
volume_offset	dict
volume_offset.(x,y,z)	int	config metadata	0
x_rotation_offset	float	config metadata	0
tilt_offset	float	config metadata	0
affine_transformation_matrix	4X4 float matrix	config metadata	identity matrix
is_canonical	bool	config metadata	false
alignment_file_path	str	-	None
tilt_file_path	str	-	None
deposition_id	int	config
per_section_alignment_parameters	list
psap.[].z_index	int	TBD	TBD	TBD
psap.[].x_offset	float	xf file	None	columns[n-1]
psap.[].y_offset	float	xf file	None	columns[n]
psap.[].in_plane_rotation	(float, float, float, float)	xf file	None	columns[1:4]
psap.[].beam_tilt	float	TBD	TBD	TBD
psap.[].tilt_angle	float	tlt file	None
psap.[].volume_x_rotation	float	tltx file	0

If there are no alignment files available, the per_section_alignment_parameters will be an empty list with the default values for the other fields.

Frames

• Update the location where .mdoc and .rawtlt to /<dataset-id>/<run-name>/Frames
• Update the names to <run_name>.mdoc or <run_name>.rawtlt respectively

Gains

• Update gain files to be stored in /<dataset-id>/<run-name>/Gain
• Update the naming of the gain file to be <name-in-source>.<ext>

[junxini]

@manasaV3 to break down into 2 tickets and point both

[manasaV3]

beam_tilt to be supported as a part of the aln files for alignment. Not needed for this feature.

[manasaV3]

Update the names to .mdoc or .rawtlt respectively

We are not going to update the mdoc and rawtlt files to run name, as there are edge cases where we might have multiple of those files. So, we are gonna continue retaining the source file name as a part of their names.

[manasaV3]

Update the location of .rawtlt to /<dataset-id>/<run-name>/Frames

rawtlts files will continue to be stored in Tiltseries folder, to establish the relationship between them and the tiltseries.