adding scripts for TM

[shruthivis]

• rename to run_pytom_pipeline, rename tm_modules dir
• fix spacing and line char length
• add comments for config file inputs

• pickET/evaluations/modules/metadata.py

  Line 34 in e2ace2e

  voxel_size = float(mrc.voxel_size.x)

  voxel_size not in x
• reorg to have template dir and dirs for each tomogram for a given experiment ID

• pickET/evaluations/modules/metadata.py

  Line 131 in e2ace2e

  f"{basename}_mask.mrc"

  see if required to rename pickET
• "rawtlt": sidecars["rawtlt"], and tilt_info is redundant

• pickET/evaluations/modules/metadata.py

  Line 63 in e2ace2e

  sidecars = discover_sidecar_files(mrc_path)

  is redundant with a previous call
• build_dataset -> rename to get_metadata or build_metadata
• fix get_particle_diameter
• remove brackets for variable assignment
• if extraction_particle_diameter == "auto": : make it not have auto args
• compute functions inline (e.g. particle_diameter_voxels, box_size)
• avoid unnecessary prints
• consider minimizing number of files in modules.
• see if the moving of files in extraction command can be done in one step (outsourced to a function)
• extraction diameter function: where the particle dia is elongated and we want the distance along the short axis: make it radius of gyration, with a note that we may have to change this manually if required

• pickET/evaluations/run_pipeline.py

  Line 856 in df2e6d0

  # CONVERSION

  what conversion

[shruthivis]

• estimate_roc: --particle-diameter PARTICLE_DIAMETER: set to extraction diameter
• estimate_roc: -n based on number of particles extracted * 3.
• add conversion.py contents to evaluation.

[shruthivis]

• extraction dia - add the code for rgyr, take from config if number not there