From 43df8f3fdcc41b798a1d95fb221cd8668fb9305f Mon Sep 17 00:00:00 2001 From: Manasa Venkatakrishnan <14958785+manasaV3@users.noreply.github.com> Date: Thu, 26 Sep 2024 09:37:15 -0700 Subject: [PATCH] fix: Fixing the values for key photo literals (#286) Fixing the values for key photo literals --- ingestion_tools/dataset_configs/10000.yaml | 5 ----- ingestion_tools/dataset_configs/10001.yaml | 5 ----- ingestion_tools/dataset_configs/10002.yaml | 5 ----- ingestion_tools/dataset_configs/10003.yaml | 5 ----- ingestion_tools/dataset_configs/10004.yaml | 5 ----- ingestion_tools/dataset_configs/10005.yaml | 5 ----- ingestion_tools/dataset_configs/10006.yaml | 5 ----- ingestion_tools/dataset_configs/10007.yaml | 5 ----- ingestion_tools/dataset_configs/10008.yaml | 5 ----- ingestion_tools/dataset_configs/10009.yaml | 5 ----- ingestion_tools/dataset_configs/10010.yaml | 5 ----- ingestion_tools/dataset_configs/10011_draft.yaml | 5 ----- .../scripts/tests/fixtures/annotations/anno_config.yaml | 5 ----- ingestion_tools/scripts/tests/fixtures/dataset1.yaml | 5 ----- .../scripts/tests/fixtures/voxel_spacing/mrc_header.yaml | 5 ----- .../tests/fixtures/voxel_spacing/overrides_by_run.yaml | 5 ----- .../scripts/tests/fixtures/voxel_spacing/tomo_metadata.yaml | 5 ----- .../tests/fixtures/voxel_spacing/tomo_run_data_map.yaml | 5 ----- 18 files changed, 90 deletions(-) diff --git a/ingestion_tools/dataset_configs/10000.yaml b/ingestion_tools/dataset_configs/10000.yaml index d10a0d1ec..6c77c5fe9 100644 --- a/ingestion_tools/dataset_configs/10000.yaml +++ b/ingestion_tools/dataset_configs/10000.yaml @@ -453,11 +453,6 @@ gains: - sources: - source_glob: list_glob: frames/CountRef.dm4 -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10001.yaml b/ingestion_tools/dataset_configs/10001.yaml index fdd28f03a..a2b5061a4 100644 --- a/ingestion_tools/dataset_configs/10001.yaml +++ b/ingestion_tools/dataset_configs/10001.yaml @@ -423,11 +423,6 @@ gains: - sources: - source_glob: list_glob: VPP/frames/CountRef_{run_name}.dm4 -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10002.yaml b/ingestion_tools/dataset_configs/10002.yaml index 9866b38d2..bd6a95407 100644 --- a/ingestion_tools/dataset_configs/10002.yaml +++ b/ingestion_tools/dataset_configs/10002.yaml @@ -161,11 +161,6 @@ gains: - sources: - source_glob: list_glob: CountRef_{mapped_frame_name}-range.dm4 -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10003.yaml b/ingestion_tools/dataset_configs/10003.yaml index 4ab11c5fb..401540182 100644 --- a/ingestion_tools/dataset_configs/10003.yaml +++ b/ingestion_tools/dataset_configs/10003.yaml @@ -117,11 +117,6 @@ gains: - sources: - source_glob: list_glob: frames/{run_name}/*.dm4 -key_images: -- sources: - - literal: - value: - - from_tomogram runs: - sources: - source_glob: diff --git a/ingestion_tools/dataset_configs/10004.yaml b/ingestion_tools/dataset_configs/10004.yaml index 608b43729..2c291cdc2 100644 --- a/ingestion_tools/dataset_configs/10004.yaml +++ b/ingestion_tools/dataset_configs/10004.yaml @@ -158,11 +158,6 @@ gains: - sources: - source_glob: list_glob: gain/gain.mrc -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10005.yaml b/ingestion_tools/dataset_configs/10005.yaml index 0827ccea4..df41fc8aa 100644 --- a/ingestion_tools/dataset_configs/10005.yaml +++ b/ingestion_tools/dataset_configs/10005.yaml @@ -127,11 +127,6 @@ depositions: - literal: value: - 10005 -key_images: -- sources: - - literal: - value: - - from_tomogram runs: - sources: - source_glob: diff --git a/ingestion_tools/dataset_configs/10006.yaml b/ingestion_tools/dataset_configs/10006.yaml index f45dd6663..aaad9384f 100644 --- a/ingestion_tools/dataset_configs/10006.yaml +++ b/ingestion_tools/dataset_configs/10006.yaml @@ -159,11 +159,6 @@ gains: - sources: - source_glob: list_glob: gainRef/CountRef_mapped-{run_name}_acquisition-order_-0.0.dm4 -key_images: -- sources: - - literal: - value: - - from_tomogram runs: - sources: - source_glob: diff --git a/ingestion_tools/dataset_configs/10007.yaml b/ingestion_tools/dataset_configs/10007.yaml index 2cace3631..42f553a73 100644 --- a/ingestion_tools/dataset_configs/10007.yaml +++ b/ingestion_tools/dataset_configs/10007.yaml @@ -120,11 +120,6 @@ gains: - sources: - source_glob: list_glob: '{run_name}/*.gain' -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10008.yaml b/ingestion_tools/dataset_configs/10008.yaml index 3d530b3ed..28b7bc0c5 100644 --- a/ingestion_tools/dataset_configs/10008.yaml +++ b/ingestion_tools/dataset_configs/10008.yaml @@ -162,11 +162,6 @@ frames: - sources: - source_glob: list_glob: tomo/raw_stacks/{mapped_ts_name}/frames/*{mapped_frame_name}_*.tif -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10009.yaml b/ingestion_tools/dataset_configs/10009.yaml index 8c99c1e93..c8dbdf47b 100644 --- a/ingestion_tools/dataset_configs/10009.yaml +++ b/ingestion_tools/dataset_configs/10009.yaml @@ -292,11 +292,6 @@ frames: - sources: - source_glob: list_glob: Tomo{run_name}/raw_data/raw_frames/*.mrc.bz2 -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/dataset_configs/10010.yaml b/ingestion_tools/dataset_configs/10010.yaml index 6ef8f5a78..93cf0c60d 100644 --- a/ingestion_tools/dataset_configs/10010.yaml +++ b/ingestion_tools/dataset_configs/10010.yaml @@ -145,11 +145,6 @@ frames: - sources: - source_glob: list_glob: frames/{run_name}_*.tif -key_images: -- sources: - - literal: - value: - - from_tomogram runs: - sources: - source_glob: diff --git a/ingestion_tools/dataset_configs/10011_draft.yaml b/ingestion_tools/dataset_configs/10011_draft.yaml index 9880ef5f8..ae59e24e6 100644 --- a/ingestion_tools/dataset_configs/10011_draft.yaml +++ b/ingestion_tools/dataset_configs/10011_draft.yaml @@ -92,11 +92,6 @@ gains: - sources: - source_glob: list_glob: frames/CountRef.dm4 -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/scripts/tests/fixtures/annotations/anno_config.yaml b/ingestion_tools/scripts/tests/fixtures/annotations/anno_config.yaml index b2403a1f2..a11c9aa05 100644 --- a/ingestion_tools/scripts/tests/fixtures/annotations/anno_config.yaml +++ b/ingestion_tools/scripts/tests/fixtures/annotations/anno_config.yaml @@ -55,11 +55,6 @@ gains: - sources: - source_glob: list_glob: '' -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/scripts/tests/fixtures/dataset1.yaml b/ingestion_tools/scripts/tests/fixtures/dataset1.yaml index 04bb96ec4..a9dd43052 100644 --- a/ingestion_tools/scripts/tests/fixtures/dataset1.yaml +++ b/ingestion_tools/scripts/tests/fixtures/dataset1.yaml @@ -129,11 +129,6 @@ gains: list_globs: - VPP/frames/CountRef_{run_name}.dm4 - VPP/frames/CountRef_{run_name}.gain -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/mrc_header.yaml b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/mrc_header.yaml index 67ece3eb4..e0d0fab9a 100644 --- a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/mrc_header.yaml +++ b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/mrc_header.yaml @@ -43,11 +43,6 @@ gains: - sources: - source_glob: list_glob: '' -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/overrides_by_run.yaml b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/overrides_by_run.yaml index c804ccdb8..3d2a9e497 100644 --- a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/overrides_by_run.yaml +++ b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/overrides_by_run.yaml @@ -43,11 +43,6 @@ gains: - sources: - source_glob: list_glob: '' -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_metadata.yaml b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_metadata.yaml index b3bf8d5e3..16da57047 100644 --- a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_metadata.yaml +++ b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_metadata.yaml @@ -43,11 +43,6 @@ gains: - sources: - source_glob: list_glob: '' -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: diff --git a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_run_data_map.yaml b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_run_data_map.yaml index 6c7cb8f3f..1572bea47 100644 --- a/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_run_data_map.yaml +++ b/ingestion_tools/scripts/tests/fixtures/voxel_spacing/tomo_run_data_map.yaml @@ -43,11 +43,6 @@ gains: - sources: - source_glob: list_glob: '' -key_images: -- sources: - - literal: - value: - - from_tomogram rawtilts: - sources: - source_multi_glob: