FTIR Observation Log

A FTIR observation log links a sampling log to the bruker invenio s ftir provision. FTIR requires milled samples, so the preparation is ds2m (dried, sieved to 2 mm, then milled) rather than the ds2 used by the NIR instruments.

Prerequisites

• Manage FTIR spectrometer must be complete.
• Sampling logs must exist from Load dataset metadata.
• Preparation, preservation, and storage utility records must exist from Load utility data.

Notebook cell

In load_ai4sh_spectral_data.ipynb, the Manage FTIR observation log cell runs:

job_file = 'import_data/FTIR_spectra/job_ftir_observation_log.json'

structured_process_D, scheme_params_D = Initiate_process(notebook_path, scheme_file, job_file)

if structured_process_D is not None:
    Run_process(structured_process_D, scheme_params_D)

Job file

Path: ./ai4sh/import_data/FTIR_spectra/job_ftir_observation_log.json

{
  "process": {
    "job_folder": "import_data/FTIR_spectra/observation_log",
    "process_sub_folder": "process",
    "pilot_file": "xspatula_add_observation_log_pilot.txt"
  }
}

Process file example

Path: ./ai4sh/import_data/FTIR_spectra/observation_log/process/ai4sh_ch_lens_2026@ftir_ds2m_observation_log.json

{
  "process": [
    {
      "process": "manage_observation_log",
      "parameters": {
        "sampling_log_id__sampling_log_name": "ai4sh_ch_lens_2025",
        "provision_id__provision_name": "bruker invenio s ftir",
        "name": "ai4sh_ch_lens_2026@ftir_ds2m",
        "contact_name": "thomas gumbricht",
        "contact_email": "thomas.gumbricht@natgeo.su.se",
        "preparation_id__preparation_name": "ds2m",
        "preservation_id__preservation_name": "ds2",
        "storage_id__storage_name": "amb",
        "laboratory": 1
      }
    }
  ]
}

14 observation log process files — one per field site.

Parameters

Parameter	Description
sampling_log_id__sampling_log_name	FK lookup: parent sampling log
provision_id__provision_name	FK lookup: bruker invenio s ftir
name	Observation log name — pattern: <sampling_log_year+1>@ftir_<preparation>
contact_name	Responsible person
contact_email	Contact email
preparation_id__preparation_name	FK lookup: ds2m (dried, sieved 2 mm, milled)
preservation_id__preservation_name	FK lookup: preservation method
storage_id__storage_name	FK lookup: storage condition
laboratory	Integer flag — 1 for laboratory observations

Next step

Proceed to Manage FTIR observation.