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chore: Fix/Complete available alignments for existing datasets #318

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merged 5 commits into from
Oct 16, 2024
Merged

chore: Fix/Complete available alignments for existing datasets #318

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045d970
fix available alignments for 10001, 10002, 10003
uermel Oct 16, 2024
fc16d8f
add rawtlts for 10004
uermel Oct 16, 2024
b7299be
add missing tlt for 10007
uermel Oct 16, 2024
ee72a7d
add missing rawtlt for 10008
uermel Oct 16, 2024
ec6ecf6
add missing rawtlt for 10009
uermel Oct 16, 2024
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1 change: 1 addition & 0 deletions ingestion_tools/dataset_configs/10000.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ alignments:
- source_multi_glob:
list_globs:
- metadata/{run_name}.xf
- metadata/{run_name}.tlt
annotations:
- metadata:
annotation_method: Cumulative template-matching trained 2D CNN predictions + visual
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1 change: 1 addition & 0 deletions ingestion_tools/dataset_configs/10001.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ alignments:
- source_multi_glob:
list_globs:
- metadata/{run_name}.xf
- metadata/{run_name}.tlt
annotations:
- metadata:
annotation_method: Cumulative template-matching trained 2D CNN predictions + visual
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6 changes: 6 additions & 0 deletions ingestion_tools/dataset_configs/10002.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ alignments:
- source_multi_glob:
list_globs:
- metadata/{run_name}_sq_df_sorted_fid.xf
- metadata/{run_name}.tlt
annotations:
- metadata:
annotation_method: manual segmentation
Expand Down Expand Up @@ -186,6 +187,11 @@ gains:
- sources:
- source_glob:
list_glob: CountRef_{mapped_frame_name}-range.dm4
rawtilts:
- sources:
- source_multi_glob:
list_globs:
- metadata/{run_name}.rawtlt
runs:
- sources:
- source_glob:
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5 changes: 5 additions & 0 deletions ingestion_tools/dataset_configs/10004.yaml
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Expand Up @@ -167,6 +167,11 @@ gains:
- sources:
- source_glob:
list_glob: gain/gain.mrc
rawtilts:
- sources:
- source_multi_glob:
list_globs:
- '{run_name}/{run_name}.mdoc-dose_filt.rawtlt'
runs:
- sources:
- source_glob:
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1 change: 1 addition & 0 deletions ingestion_tools/dataset_configs/10007.yaml
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Expand Up @@ -5,6 +5,7 @@ alignments:
- source_multi_glob:
list_globs:
- '{run_name}/AreTomo/*_dose-filt.xf'
- '{run_name}/AreTomo/*_dose-filt.tlt'
annotations:
- metadata:
annotation_method: crYOLO picking
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7 changes: 7 additions & 0 deletions ingestion_tools/dataset_configs/10008.yaml
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Expand Up @@ -171,6 +171,13 @@ frames:
- sources:
- source_glob:
list_glob: tomo/raw_stacks/{mapped_ts_name}/frames/*{mapped_frame_name}_*.tif

rawtilts:
- sources:
- source_multi_glob:
list_globs:
- 'tomo/raw_stacks/{mapped_ts_name}/imod/{mapped_frame_name}-.*.rawtlt'

runs:
- sources:
- source_glob:
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7 changes: 7 additions & 0 deletions ingestion_tools/dataset_configs/10009.yaml
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Expand Up @@ -301,6 +301,13 @@ frames:
- sources:
- source_glob:
list_glob: Tomo{run_name}/raw_data/raw_frames/*.mrc.bz2

rawtilts:
- sources:
- source_multi_glob:
list_globs:
- 'Tomo{run_name}/raw_data/imod_metadata/*.rawtlt'

runs:
- sources:
- source_glob:
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