feat: Creating standardized tomo config #354
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| datasets: | ||
| - sources: | ||
| - destination_glob: | ||
| list_glob: '{output_path}/*' | ||
| match_regex: '/\d*$' | ||
| name_regex: (.*) | ||
| depositions: | ||
| - metadata: | ||
| authors: &id001 | ||
| - ORCID: 0000-0003-4685-037X | ||
| corresponding_author_status: true | ||
| name: Utz Heinrich Ermel | ||
| primary_author_status: true | ||
| dates: &id002 | ||
| deposition_date: '2024-10-15' | ||
| last_modified_date: '2024-10-15' | ||
| release_date: '2024-10-15' | ||
| deposition_description: Standardized tomograms. | ||
| deposition_identifier: 10311 | ||
| deposition_title: Standardized tomograms | ||
| deposition_types: | ||
| - tomogram | ||
| sources: | ||
| - literal: | ||
| value: | ||
| - 10311 | ||
| runs: | ||
| - sources: | ||
| - destination_glob: | ||
| list_glob: '{dataset_output_path}/*' | ||
| match_regex: .* | ||
| name_regex: (.*) | ||
| exclude: | ||
| - Images | ||
| - dataset_metadata.json | ||
| standardization_config: | ||
| deposition_id: 10311 | ||
| source_prefix: CZII/standard_tomograms_v2/ | ||
| version: 1.1.0 | ||
| voxel_spacings: | ||
| - sources: | ||
| - source_glob: | ||
| list_glob: '{dataset_name}_{run_name}/*' | ||
| match_regex: '[\d\.]{5,7}$' | ||
| name_regex: '([\d\.]{5,7})$' | ||
| exclude: | ||
| - logs | ||
| alignments: | ||
| - metadata: | ||
| alignment_type: LOCAL | ||
| format: ARETOMO3 | ||
| method_type: projection_matching | ||
| is_portal_standard: true | ||
| offset: | ||
| x: 0 | ||
| y: 0 | ||
| z: 0 | ||
| x_rotation_offset: 0 | ||
| tilt_offset: 0 | ||
| sources: | ||
| - source_glob: | ||
| list_glob: '{dataset_name}_{run_name}/*/outputs/aretomo/reconstruct_only/{run_name}.aln' | ||
|
There was a problem hiding this comment. Updates the list_glob from Confirmed with Utz that we won't have more than one voxel spacing available for a run as the voxel spacing is generated using this logic. :) |
||
| tomograms: | ||
| - metadata: | ||
| align_software: ARETOMO3 | ||
| authors: *id001 | ||
| ctf_corrected: true | ||
| fiducial_alignment_status: FIDUCIAL | ||
| offset: | ||
| x: 0 | ||
| y: 0 | ||
| z: 0 | ||
| processing: filtered | ||
| processing_software: AreTomo3 | ||
| reconstruction_method: WBP | ||
| reconstruction_software: AreTomo3 | ||
| tomogram_version: 1.0 | ||
| voxel_spacing: float {voxel_spacing_name} | ||
| is_visualization_default: true | ||
| is_portal_standard: true | ||
| dates: *id002 | ||
| sources: | ||
| - source_glob: | ||
| list_glob: '{dataset_name}_{run_name}/{voxel_spacing_name}/outputs/aretomo/reconstruct_only/{run_name}_Vol.zarr' | ||
| - metadata: | ||
| align_software: ARETOMO3 | ||
| authors: *id001 | ||
| ctf_corrected: true | ||
| fiducial_alignment_status: FIDUCIAL | ||
| offset: | ||
| x: 0 | ||
| y: 0 | ||
| z: 0 | ||
| processing: raw | ||
| processing_software: AreTomo3 | ||
| reconstruction_method: WBP | ||
| reconstruction_software: AreTomo3 | ||
| tomogram_version: 1.0 | ||
| voxel_spacing: float {voxel_spacing_name} | ||
| is_visualization_default: false | ||
| is_standardized: true | ||
| dates: *id002 | ||
| sources: | ||
| - source_glob: | ||
| list_glob: '{dataset_name}_{run_name}/{voxel_spacing_name}/outputs/aretomo/reconstruct_only/{run_name}_2ND_Vol.zarr' | ||
| match_regex: .* | ||
| - metadata: | ||
| align_software: ARETOMO3 | ||
| authors: *id001 | ||
| ctf_corrected: true | ||
| fiducial_alignment_status: FIDUCIAL | ||
| offset: | ||
| x: 0 | ||
| y: 0 | ||
| z: 0 | ||
| processing: raw | ||
| processing_software: AreTomo3 | ||
| reconstruction_method: SART | ||
| reconstruction_software: AreTomo3 | ||
| tomogram_version: 1.0 | ||
| voxel_spacing: float {voxel_spacing_name} | ||
| is_visualization_default: false | ||
| is_standardized: true | ||
| dates: *id002 | ||
| sources: | ||
| - source_glob: | ||
| list_glob: '{dataset_name}_{run_name}/{voxel_spacing_name}/outputs/aretomo/reconstruct_only/{run_name}_3RD_Vol.zarr' | ||
| match_regex: .* | ||
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Added support for
output_pathin the glob variables.