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Extend to input by Tescan instruments#58

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GGoetzelmann merged 45 commits into
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wip_semmapping_tescan
Aug 1, 2025
Merged

Extend to input by Tescan instruments#58
GGoetzelmann merged 45 commits into
developmentfrom
wip_semmapping_tescan

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@gabinoumbe

@gabinoumbe gabinoumbe commented Jul 31, 2025

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This PR is an extension to Tescan input. It introduces significant improvements to the tomography mapping pipeline by adding support for multiple sources and parsers, and enriching the output with a fileLink field in image metadata (md) records. The fileLink record also prepares the code for transparency improvement in how images metadata are grouped within datasets.

New parsers:

  • Dataset_infoParser
  • TomographyProjectParser
  • TxtParser

New input map files:

  • input map_tescan

Changes made:

  1. MapFileReader updated:
  • sources and parser fields in the map file now accept either a single string or a list.
  • Ensures that if both are lists, their lengths must match (1-to-1 mapping between source and parser).
  • If only one parser is provided for multiple sources, it is replicated across all sources.
  1. InputReader updated:
  • Handles pairs of (source, parser) instead of a single parser and a single source.
  • Adjust retrieve_setup_info and retrieve_run_info logics to parse each (source, parser) pair.
  1. Output Improvements
  • Add fileLink (reflected filePath) of every image in the final output while preserving the Identifier type.
  • Ensures that OutputWriter can stitch together a list of setup_infos and a list of run_infos.

This PR closes #36 and #17

gabinoumbe and others added 30 commits February 27, 2025 14:27
# Conflicts:
#	mapping_cli.py
#	src/resources/maps/acquisition_map.csv
#	src/resources/maps/image_map.csv
(for better or worse)
# Conflicts:
#	requirements.txt
…ng based on file extension anymore. Function still included. More detailed debug logging
Resulting fix for preprocessor date handling
@gabinoumbe gabinoumbe temporarily deployed to wip_semmapping_tescan August 1, 2025 12:51 — with GitHub Actions Inactive
@gabinoumbe gabinoumbe temporarily deployed to wip_semmapping_tescan August 1, 2025 12:51 — with GitHub Actions Inactive
@gabinoumbe gabinoumbe temporarily deployed to wip_semmapping_tescan August 1, 2025 12:51 — with GitHub Actions Inactive
@gabinoumbe gabinoumbe temporarily deployed to wip_semmapping_tescan August 1, 2025 12:51 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:04 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:04 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:04 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:04 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:15 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:15 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:16 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:16 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:28 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:28 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:29 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:29 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:31 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:31 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann temporarily deployed to wip_semmapping_tescan August 1, 2025 15:31 — with GitHub Actions Inactive
@GGoetzelmann GGoetzelmann deployed to wip_semmapping_tescan August 1, 2025 15:31 — with GitHub Actions Active
@GGoetzelmann GGoetzelmann merged commit 1a45229 into development Aug 1, 2025
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@GGoetzelmann GGoetzelmann mentioned this pull request Aug 4, 2025
@GGoetzelmann GGoetzelmann deleted the wip_semmapping_tescan branch August 5, 2025 15:31
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