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

* fix available alignments for 10001, 10002, 10003 * add rawtlts for 10004 * add missing tlt for 10007 * add missing rawtlt for 10008 * add missing rawtlt for 10009
chanzuckerberg · Oct 16, 2024 · 7490d36 · 7490d36
1 parent 123c651
commit 7490d36
Show file tree

Hide file tree

Showing 7 changed files with 28 additions and 0 deletions.
diff --git 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
@@ -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
@@ -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:

diff --git 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:

diff --git 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

diff --git 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:

diff --git 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: