From 045d97045d86d9a45b803151cdff9e1554704127 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 15 Oct 2024 17:57:23 -0700 Subject: [PATCH 1/5] fix available alignments for 10001, 10002, 10003 --- ingestion_tools/dataset_configs/10000.yaml | 1 + ingestion_tools/dataset_configs/10001.yaml | 1 + ingestion_tools/dataset_configs/10002.yaml | 6 ++++++ 3 files changed, 8 insertions(+) diff --git a/ingestion_tools/dataset_configs/10000.yaml b/ingestion_tools/dataset_configs/10000.yaml index 0acc7ef20..e53e3dc82 100644 --- a/ingestion_tools/dataset_configs/10000.yaml +++ b/ingestion_tools/dataset_configs/10000.yaml @@ -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 diff --git a/ingestion_tools/dataset_configs/10001.yaml b/ingestion_tools/dataset_configs/10001.yaml index 721480ea8..3a08dac70 100644 --- a/ingestion_tools/dataset_configs/10001.yaml +++ b/ingestion_tools/dataset_configs/10001.yaml @@ -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 diff --git a/ingestion_tools/dataset_configs/10002.yaml b/ingestion_tools/dataset_configs/10002.yaml index cf951cc49..06fa31f3d 100644 --- a/ingestion_tools/dataset_configs/10002.yaml +++ b/ingestion_tools/dataset_configs/10002.yaml @@ -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 @@ -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: From fc16d8fcdf8582fa00f0be56d8ef4109faab3edb Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 15 Oct 2024 18:05:42 -0700 Subject: [PATCH 2/5] add rawtlts for 10004 --- ingestion_tools/dataset_configs/10004.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ingestion_tools/dataset_configs/10004.yaml b/ingestion_tools/dataset_configs/10004.yaml index 50604baa8..69d3be7d8 100644 --- a/ingestion_tools/dataset_configs/10004.yaml +++ b/ingestion_tools/dataset_configs/10004.yaml @@ -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: From b7299bec46f9b4e76da60dec3a37166ec3981e9c Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 15 Oct 2024 18:08:03 -0700 Subject: [PATCH 3/5] add missing tlt for 10007 --- ingestion_tools/dataset_configs/10007.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/ingestion_tools/dataset_configs/10007.yaml b/ingestion_tools/dataset_configs/10007.yaml index 181f23529..468482910 100644 --- a/ingestion_tools/dataset_configs/10007.yaml +++ b/ingestion_tools/dataset_configs/10007.yaml @@ -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 From ee72a7dfe59e6383987d21b137054a43348ab9d9 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 15 Oct 2024 18:12:17 -0700 Subject: [PATCH 4/5] add missing rawtlt for 10008 --- ingestion_tools/dataset_configs/10008.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/ingestion_tools/dataset_configs/10008.yaml b/ingestion_tools/dataset_configs/10008.yaml index 76199977b..e49fe8cdf 100644 --- a/ingestion_tools/dataset_configs/10008.yaml +++ b/ingestion_tools/dataset_configs/10008.yaml @@ -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: From ec6ecf6cf33870e15664c07e2a0ea5c773a0a6ad Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 15 Oct 2024 18:15:15 -0700 Subject: [PATCH 5/5] add missing rawtlt for 10009 --- ingestion_tools/dataset_configs/10009.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/ingestion_tools/dataset_configs/10009.yaml b/ingestion_tools/dataset_configs/10009.yaml index 4d1bd95f0..fba05a91a 100644 --- a/ingestion_tools/dataset_configs/10009.yaml +++ b/ingestion_tools/dataset_configs/10009.yaml @@ -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: