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feat: Updates to the alignment entity #298

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merged 6 commits into from
Oct 2, 2024
Merged

feat: Updates to the alignment entity #298

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607fe60
Updates to schema and template
manasaV3 Oct 1, 2024
f8414ea
Fixing tests
manasaV3 Oct 1, 2024
10c9324
Adding files to alignments metadata
manasaV3 Oct 1, 2024
8375246
Update the alignment configs method type
manasaV3 Oct 1, 2024
98df25f
Fixing typo
manasaV3 Oct 2, 2024
be6dc25
Adding undefined alignment_method_type
manasaV3 Oct 2, 2024
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16 changes: 1 addition & 15 deletions ingestion_tools/dataset_configs/10000.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
alignments:
- metadata:
format: IMOD
method_type: patch_tracking
sources:
- source_multi_glob:
list_globs:
Expand Down Expand Up @@ -62,7 +63,6 @@ annotations:
columns: xyz
file_format: csv
glob_string: particle_lists/{run_name}_fas.csv

is_visualization_default: false
- metadata:
annotation_method: Cumulative template-matching trained 2D CNN predictions + visual
Expand All @@ -85,7 +85,6 @@ annotations:
columns: xyz
file_format: csv
glob_string: particle_lists/{run_name}_cyto_ribosomes.csv

is_visualization_default: true
- metadata:
annotation_method: spectrum equalization filter + 2D CNN prediction + manual correction
Expand All @@ -106,7 +105,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 1
- metadata:
Expand All @@ -128,7 +126,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: true
mask_label: 2
- metadata:
Expand All @@ -150,7 +147,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 3
- metadata:
Expand All @@ -172,7 +168,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: true
mask_label: 4
- metadata:
Expand All @@ -194,7 +189,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: true
mask_label: 5
- metadata:
Expand All @@ -216,7 +210,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: true
mask_label: 6
- metadata:
Expand All @@ -238,7 +231,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 7
- metadata:
Expand All @@ -260,7 +252,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 8
- metadata:
Expand All @@ -282,7 +273,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 9
- metadata:
Expand All @@ -304,7 +294,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: true
mask_label: 10
- metadata:
Expand All @@ -326,7 +315,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 11
- metadata:
Expand All @@ -348,7 +336,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/180426_{mapped_segmask_name}.labels.mrc

is_visualization_default: false
mask_label: 13
- metadata:
Expand All @@ -370,7 +357,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_membranes.mrc

is_visualization_default: false
mask_label: 1
collection_metadata:
Expand Down
16 changes: 1 addition & 15 deletions ingestion_tools/dataset_configs/10001.yaml
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
alignments:
- metadata:
format: IMOD
method_type: patch_tracking
sources:
- source_multi_glob:
list_globs:
Expand Down Expand Up @@ -62,7 +63,6 @@ annotations:
columns: xyz
file_format: csv
glob_string: particle_lists/{run_name}_fas.csv

is_visualization_default: false
- metadata:
annotation_method: Cumulative template-matching trained 2D CNN predictions + visual
Expand All @@ -85,7 +85,6 @@ annotations:
columns: xyz
file_format: csv
glob_string: particle_lists/{run_name}_cyto_ribosomes.csv

is_visualization_default: true
- metadata:
annotation_method: manual segmentation
Expand All @@ -105,7 +104,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 1
- metadata:
Expand All @@ -126,7 +124,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: true
mask_label: 2
- metadata:
Expand All @@ -147,7 +144,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 3
- metadata:
Expand All @@ -168,7 +164,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: true
mask_label: 4
- metadata:
Expand All @@ -189,7 +184,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: true
mask_label: 5
- metadata:
Expand All @@ -210,7 +204,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: true
mask_label: 6
- metadata:
Expand All @@ -231,7 +224,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 7
- metadata:
Expand All @@ -252,7 +244,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 8
- metadata:
Expand All @@ -273,7 +264,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 9
- metadata:
Expand All @@ -294,7 +284,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: true
mask_label: 10
- metadata:
Expand All @@ -315,7 +304,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 11
- metadata:
Expand All @@ -336,7 +324,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_organelles.mrc

is_visualization_default: false
mask_label: 13
- metadata:
Expand All @@ -358,7 +345,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_membranes.mrc

is_visualization_default: false
mask_label: 1
collection_metadata:
Expand Down
3 changes: 1 addition & 2 deletions ingestion_tools/dataset_configs/10002.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ alignments:
- 625
- 1
format: IMOD
method_type: patch_tracking
sources:
- source_multi_glob:
list_globs:
Expand Down Expand Up @@ -75,7 +76,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: labels/{run_name}_actin_ground_truth.mrc

is_visualization_default: true
- metadata:
annotation_method: 2D CNN + 3D CNN hyperparameter tuning
Expand All @@ -99,7 +99,6 @@ annotations:
- SemanticSegmentationMask:
file_format: mrc
glob_string: prediction/{run_name}_*.mrc

is_visualization_default: false
collection_metadata:
- sources:
Expand Down
2 changes: 1 addition & 1 deletion ingestion_tools/dataset_configs/10004.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
alignments:
- metadata:
format: IMOD
method_type: patch_tracking
sources:
- source_multi_glob:
list_globs:
Expand Down Expand Up @@ -69,7 +70,6 @@ annotations:
columns: xyz
file_format: csv_with_header
glob_string: '{run_name}/annoRibosome_bin4.txt'

is_visualization_default: true
collection_metadata:
- sources:
Expand Down
3 changes: 1 addition & 2 deletions ingestion_tools/dataset_configs/10008.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
alignments:
- metadata:
format: IMOD
method_type: fiducial_based
sources:
- source_multi_glob:
list_globs:
Expand Down Expand Up @@ -54,7 +55,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: subtomo/hdcr/hdcr_tm_bin2_motl_12.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -76,7 +76,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: subtomo/ribo/ribo_tm_bin1_motl_12.star

is_visualization_default: true
order: xyz
collection_metadata:
Expand Down
8 changes: 1 addition & 7 deletions ingestion_tools/dataset_configs/10009.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
alignments:
- metadata:
format: IMOD
method_type: fiducial_based
sources:
- source_multi_glob:
list_globs:
Expand Down Expand Up @@ -64,7 +65,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/allmotl_S_newbin2_3.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -86,7 +86,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/allmotl_Y_newbin2_3.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -108,7 +107,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/allmotl_H_cleanbin2.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -131,7 +129,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/MTD_MIP_bin2_recentered_shiftedorg_9.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -153,7 +150,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/allmotl_B2_newbin2_3.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -175,7 +171,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/allmotl_A2_newbin2_3.star

is_visualization_default: true
order: xyz
- metadata:
Expand All @@ -197,7 +192,6 @@ annotations:
file_format: stopgap_star
filter_value: '{run_name}'
glob_string: motivelists/allmotl_D_newbin2_3.star

is_visualization_default: true
order: xyz
collection_metadata:
Expand Down
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