Fixing tomogram processing

chanzuckerberg · Mar 1, 2024 · 432132f · 432132f
1 parent 560cec4
commit 432132f
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Showing 90 changed files with 3,681 additions and 3,660 deletions.
diff --git a/ingestion_tools/dataset_configs/gjensen/10014.yaml b/ingestion_tools/dataset_configs/gjensen/10014.yaml
@@ -87,7 +87,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10015.yaml b/ingestion_tools/dataset_configs/gjensen/10015.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: Weighted back projection
   reconstruction_software: IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10016.yaml b/ingestion_tools/dataset_configs/gjensen/10016.yaml
@@ -87,7 +87,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10017.yaml b/ingestion_tools/dataset_configs/gjensen/10017.yaml
@@ -85,7 +85,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10018.yaml b/ingestion_tools/dataset_configs/gjensen/10018.yaml
@@ -64,7 +64,7 @@ tomograms:
   reconstruction_software: IMOD
   fiducial_alignment_status: FIDUCIAL
   ctf_corrected: null
-  processing: IMOD, SIRT-like
+  processing: raw
   processing_software: IMOD
   align_softwares:
   - IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10019.yaml b/ingestion_tools/dataset_configs/gjensen/10019.yaml
@@ -63,7 +63,7 @@ tomograms:
   reconstruction_software: IMOD
   fiducial_alignment_status: FIDUCIAL
   ctf_corrected: null
-  processing: IMOD, SIRT-like
+  processing: raw
   processing_software: IMOD
   align_softwares:
   - IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10020.yaml b/ingestion_tools/dataset_configs/gjensen/10020.yaml
@@ -88,7 +88,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: IMOD
+  processing: raw
   processing_software: IMOD
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10021.yaml b/ingestion_tools/dataset_configs/gjensen/10021.yaml
@@ -62,8 +62,7 @@ tomograms:
   reconstruction_software: novaCTF
   fiducial_alignment_status: FIDUCIAL
   ctf_corrected: true
-  processing: ctffind4, novaCTF, custom bash and Matlab scripts;IMOD, ctffind4, novaCTF,
-    custom bash and Matlab scripts
+  processing: raw
   processing_software: novaCTF
   align_softwares:
   - IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10023.yaml b/ingestion_tools/dataset_configs/gjensen/10023.yaml
@@ -84,7 +84,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10039.yaml b/ingestion_tools/dataset_configs/gjensen/10039.yaml
@@ -65,7 +65,7 @@ tomograms:
   reconstruction_software: IMOD
   fiducial_alignment_status: FIDUCIAL
   ctf_corrected: null
-  processing: Raptor
+  processing: raw
   processing_software: IMOD
   align_softwares:
   - RAPTOR

diff --git a/ingestion_tools/dataset_configs/gjensen/10042.yaml b/ingestion_tools/dataset_configs/gjensen/10042.yaml
@@ -90,7 +90,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10043.yaml b/ingestion_tools/dataset_configs/gjensen/10043.yaml
@@ -87,7 +87,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10044.yaml b/ingestion_tools/dataset_configs/gjensen/10044.yaml
@@ -87,7 +87,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10045.yaml b/ingestion_tools/dataset_configs/gjensen/10045.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10046.yaml b/ingestion_tools/dataset_configs/gjensen/10046.yaml
@@ -69,7 +69,7 @@ tomograms:
   reconstruction_software: IMOD
   fiducial_alignment_status: FIDUCIAL
   ctf_corrected: null
-  processing: Raptor
+  processing: raw
   processing_software: IMOD
   align_softwares:
   - RAPTOR

diff --git a/ingestion_tools/dataset_configs/gjensen/10047.yaml b/ingestion_tools/dataset_configs/gjensen/10047.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10048.yaml b/ingestion_tools/dataset_configs/gjensen/10048.yaml
@@ -87,7 +87,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10049.yaml b/ingestion_tools/dataset_configs/gjensen/10049.yaml
@@ -87,7 +87,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10050.yaml b/ingestion_tools/dataset_configs/gjensen/10050.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10051.yaml b/ingestion_tools/dataset_configs/gjensen/10051.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10052.yaml b/ingestion_tools/dataset_configs/gjensen/10052.yaml
@@ -88,7 +88,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: Weighted back projection
   reconstruction_software: IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10054.yaml b/ingestion_tools/dataset_configs/gjensen/10054.yaml
@@ -83,7 +83,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10055.yaml b/ingestion_tools/dataset_configs/gjensen/10055.yaml
@@ -83,7 +83,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10062.yaml b/ingestion_tools/dataset_configs/gjensen/10062.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10064.yaml b/ingestion_tools/dataset_configs/gjensen/10064.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10065.yaml b/ingestion_tools/dataset_configs/gjensen/10065.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10066.yaml b/ingestion_tools/dataset_configs/gjensen/10066.yaml
@@ -90,7 +90,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10068.yaml b/ingestion_tools/dataset_configs/gjensen/10068.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10069.yaml b/ingestion_tools/dataset_configs/gjensen/10069.yaml
@@ -90,7 +90,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10070.yaml b/ingestion_tools/dataset_configs/gjensen/10070.yaml
@@ -90,7 +90,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10074.yaml b/ingestion_tools/dataset_configs/gjensen/10074.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10075.yaml b/ingestion_tools/dataset_configs/gjensen/10075.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10077.yaml b/ingestion_tools/dataset_configs/gjensen/10077.yaml
@@ -90,7 +90,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10080.yaml b/ingestion_tools/dataset_configs/gjensen/10080.yaml
@@ -89,7 +89,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10081.yaml b/ingestion_tools/dataset_configs/gjensen/10081.yaml
@@ -91,7 +91,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10084.yaml b/ingestion_tools/dataset_configs/gjensen/10084.yaml
@@ -91,7 +91,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10094.yaml b/ingestion_tools/dataset_configs/gjensen/10094.yaml
@@ -84,7 +84,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10097.yaml b/ingestion_tools/dataset_configs/gjensen/10097.yaml
@@ -92,7 +92,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10098.yaml b/ingestion_tools/dataset_configs/gjensen/10098.yaml
@@ -92,7 +92,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10100.yaml b/ingestion_tools/dataset_configs/gjensen/10100.yaml
@@ -80,7 +80,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10105.yaml b/ingestion_tools/dataset_configs/gjensen/10105.yaml
@@ -83,7 +83,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: Weighted back projection
   reconstruction_software: IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10106.yaml b/ingestion_tools/dataset_configs/gjensen/10106.yaml
@@ -81,7 +81,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: '{tomo-processing}'
+  processing: raw
   processing_software: '{tomo-processing_software}'
   reconstruction_method: Weighted back projection
   reconstruction_software: IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10108.yaml b/ingestion_tools/dataset_configs/gjensen/10108.yaml
@@ -83,7 +83,7 @@ tomograms:
     x: 0
     y: 0
     z: 0
-  processing: IMOD
+  processing: raw
   processing_software: IMOD
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: IMOD

diff --git a/ingestion_tools/dataset_configs/gjensen/10198.yaml b/ingestion_tools/dataset_configs/gjensen/10198.yaml
@@ -61,7 +61,7 @@ tomograms:
   reconstruction_software: IMOD
   fiducial_alignment_status: FIDUCIAL
   ctf_corrected: null
-  processing: binned 4x total then filtered 0.28 (= 4.6nm resolution cutoff)
+  processing: filtered
   processing_software: IMOD
   align_softwares:
   - RAPTOR