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feat: add ops to combine masks and mask affinities
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83 changes: 83 additions & 0 deletions
83
specs/tommy/lee_fly_cns_segmentation_test001/230608_adjust_affinities.cue
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| #AFF_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity" | ||
| #BACKUP_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity/backup_for_adjustments" | ||
|
|
||
| // #AFF_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity/cutouts/test001" | ||
| // #BACKUP_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity/cutouts/test001/backup" | ||
| #BLACKOUT_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/resin_mask_final_surgery" | ||
| #SNAP_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/img_mask_stage1_v2_64nm_try_x1_iter300_rig200_lr0.001_surgery_consecutive3" | ||
| #THRESHOLD_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/aff_mask_stage1_v2_64nm_try_x1_iter300_rig200_lr0.001_surgery" | ||
|
|
||
| "@type": "mazepa.execute_on_gcp_with_sqs" | ||
| worker_image: "us.gcr.io/zetta-lee-fly-vnc-001/zetta_utils:tmacrina_mask_affinities_x3" | ||
| worker_cluster_name: "zutils-cns" | ||
| worker_cluster_region: "us-east1" | ||
| worker_cluster_project: "zetta-lee-fly-vnc-001" | ||
| worker_resources: { | ||
| memory: "18560Mi" | ||
| } | ||
| worker_replicas: 512 | ||
| local_test: false | ||
|
|
||
| #AFF: { | ||
| "@type": "build_cv_layer" | ||
| path: #AFF_PATH | ||
| cv_kwargs: {"delete_black_uploads": false} // ws+agg require all affinities present, so cannot issue DELETES | ||
| } | ||
| #BACKUP: { | ||
| "@type": "build_cv_layer" | ||
| path: #BACKUP_PATH | ||
| info_reference_path: #AFF_PATH | ||
| } | ||
| #BLACKOUT_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #BLACKOUT_MSK_PATH | ||
| data_resolution: [256, 256, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
| #SNAP_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #SNAP_MSK_PATH | ||
| data_resolution: [64, 64, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
| #THRESHOLD_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #THRESHOLD_MSK_PATH | ||
| data_resolution: [64, 64, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
|
|
||
| #BBOX: { | ||
| "@type": "BBox3D.from_coords" | ||
| // start_coord: [1341 - 144, 288, 2990] | ||
| // end_coord: [1341, 288 + 144, 2990 + 2*13] | ||
| // resolution: [256, 256, 45] | ||
| start_coord: [0, 0, 0] | ||
| // end_coord: [4096, 4608, 7010] // actual | ||
| end_coord: [4176, 4752, 7020] // divisible by processing_chunk_size | ||
| resolution: [256, 256, 45] | ||
| } | ||
|
|
||
| target: { | ||
| "@type": "build_subchunkable_apply_flow" | ||
| // "@mode": "partial" | ||
| bbox: #BBOX | ||
| dst: #AFF | ||
| dst_resolution: [16, 16, 45] | ||
| processing_chunk_sizes: [[144 * 16, 144 * 16, 13]] | ||
| // must be one pixel for lowest-res mask in xy and >=1 in z for snap mask breaking | ||
| processing_crop_pads: [[16, 16, 1]] | ||
| processing_blend_pads: [[0, 0, 0]] | ||
| op: { | ||
| "@type": "AdjustAffinitiesOp" | ||
| } | ||
| op_kwargs: { | ||
| aff_layer: #AFF | ||
| aff_backup_layer: #BACKUP | ||
| blackout_mask_layer: #BLACKOUT_MASK | ||
| snap_mask_layer: #SNAP_MASK | ||
| threshold_mask_layer: #THRESHOLD_MASK | ||
| threshold_value: 0.85 | ||
| fill_value: 0 | ||
| } | ||
| } |
55 changes: 55 additions & 0 deletions
55
specs/tommy/lee_fly_cns_segmentation_test001/230608_detect_three_image_masks.cue
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| // Create a "snap" mask at locations of three consecutive image masks | ||
|
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| #SRC_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/img_mask_stage1_v2_64nm_try_x1_iter300_rig200_lr0.001_surgery" | ||
| #DST_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/img_mask_stage1_v2_64nm_try_x1_iter300_rig200_lr0.001_surgery_consecutive3" | ||
|
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||
| #BBOX: { | ||
| "@type": "BBox3D.from_coords" | ||
| // start_coord: [9216, 0, 4000] | ||
| // end_coord: [10240, 1024, 4064] | ||
| start_coord: [0, 0, 0] | ||
| end_coord: [16384, 18432, 7010] | ||
| resolution: [64, 64, 45] | ||
| } | ||
|
|
||
| "@type": "mazepa.execute_on_gcp_with_sqs" | ||
| worker_image: "us.gcr.io/zetta-lee-fly-vnc-001/zetta_utils:tmacrina_mask_affinities_x2" | ||
| worker_cluster_name: "zutils-cns" | ||
| worker_cluster_region: "us-east1" | ||
| worker_cluster_project: "zetta-lee-fly-vnc-001" | ||
| worker_resources: { | ||
| memory: "18560Mi" | ||
| } | ||
| worker_replicas: 128 | ||
| local_test: false | ||
|
|
||
| target: { | ||
| "@type": "build_subchunkable_apply_flow" | ||
| bbox: #BBOX | ||
| dst_resolution: [64, 64, 45] | ||
| processing_chunk_sizes: [[1024, 1024, 64]] | ||
| // need to manually set crop/pad for consecutive detection | ||
| processing_crop_pads: [[0, 0, 2]] | ||
| processing_blend_pads: [[0, 0, 0]] | ||
|
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||
| expand_bbox: true | ||
|
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| fn: { | ||
| "@type": "detect_consecutive_masks" | ||
| "@mode": "partial" | ||
| } | ||
| op_kwargs: { | ||
| src: { | ||
| "@type": "build_cv_layer" | ||
| path: #SRC_PATH | ||
| } | ||
| num_consecutive: 3 | ||
| } | ||
|
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||
| dst: { | ||
| "@type": "build_cv_layer" | ||
| path: #DST_PATH | ||
| info_reference_path: #SRC_PATH | ||
| on_info_exists: "overwrite" | ||
| } | ||
| } |
55 changes: 55 additions & 0 deletions
55
specs/tommy/lee_fly_cns_segmentation_test001/230610_detect_three_resin_masks.cue
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| // Create a "snap" mask at locations of three consecutive image masks | ||
|
|
||
| #SRC_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/resin_mask_final_surgery" | ||
| #DST_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/resin_mask_final_surgery_consecutive3" | ||
|
|
||
| #BBOX: { | ||
| "@type": "BBox3D.from_coords" | ||
| // start_coord: [9216, 0, 4000] | ||
| // end_coord: [10240, 1024, 4064] | ||
| start_coord: [0, 0, 0] | ||
| end_coord: [4096, 4608, 7010] | ||
| resolution: [256, 256, 45] | ||
| } | ||
|
|
||
| "@type": "mazepa.execute_on_gcp_with_sqs" | ||
| worker_image: "us.gcr.io/zetta-lee-fly-vnc-001/zetta_utils:tmacrina_mask_affinities_x3" | ||
| worker_cluster_name: "zutils-cns" | ||
| worker_cluster_region: "us-east1" | ||
| worker_cluster_project: "zetta-lee-fly-vnc-001" | ||
| worker_resources: { | ||
| memory: "18560Mi" | ||
| } | ||
| worker_replicas: 32 | ||
| local_test: false | ||
|
|
||
| target: { | ||
| "@type": "build_subchunkable_apply_flow" | ||
| bbox: #BBOX | ||
| dst_resolution: [256, 256, 45] | ||
| processing_chunk_sizes: [[2048, 2048, 64]] | ||
| // need to manually set crop/pad for consecutive detection | ||
| processing_crop_pads: [[0, 0, 2]] | ||
| processing_blend_pads: [[0, 0, 0]] | ||
|
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||
| expand_bbox: true | ||
|
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| fn: { | ||
| "@type": "detect_consecutive_masks" | ||
| "@mode": "partial" | ||
| } | ||
| op_kwargs: { | ||
| src: { | ||
| "@type": "build_cv_layer" | ||
| path: #SRC_PATH | ||
| } | ||
| num_consecutive: 3 | ||
| } | ||
|
|
||
| dst: { | ||
| "@type": "build_cv_layer" | ||
| path: #DST_PATH | ||
| info_reference_path: #SRC_PATH | ||
| on_info_exists: "overwrite" | ||
| } | ||
| } |
77 changes: 77 additions & 0 deletions
77
specs/tommy/lee_fly_cns_segmentation_test001/230612_copy_affinities.cue
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| #AFF_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity" | ||
| #BACKUP_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity/backup_for_adjustments" | ||
| #COPY_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity/cutouts/test002" | ||
| #AFF_COPY_PATH: #COPY_PATH + "/affinity" | ||
| #BACKUP_COPY_PATH: #COPY_PATH + "/backup" | ||
|
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||
| #BBOX: { | ||
| "@type": "BBox3D.from_coords" | ||
| start_coord: [1602, 306, 2834] | ||
| end_coord: [1602 + 18, 306 + 18, 2834 + 13] | ||
| resolution: [256, 256, 45] | ||
| } | ||
|
|
||
| "@type": "mazepa.execute_on_gcp_with_sqs" | ||
| worker_image: "us.gcr.io/zetta-lee-fly-vnc-001/zetta_utils:tmacrina_mask_affinities_x3" | ||
| worker_cluster_name: "zutils-cns" | ||
| worker_cluster_region: "us-east1" | ||
| worker_cluster_project: "zetta-lee-fly-vnc-001" | ||
| worker_resources: { | ||
| memory: "18560Mi" | ||
| } | ||
| worker_replicas: 1 | ||
| local_test: true | ||
|
|
||
| #COPY_TEMPLATE: { | ||
| "@type": "build_subchunkable_apply_flow" | ||
| bbox: #BBOX | ||
| dst_resolution: [16, 16, 45] | ||
| processing_chunk_sizes: [[144 * 2, 144 * 2, 13]] | ||
| processing_crop_pads: [[0, 0, 0]] | ||
| processing_blend_pads: [[0, 0, 0]] | ||
| expand_bbox: true | ||
|
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||
| fn: { | ||
| "@type": "lambda" | ||
| lambda_str: "lambda src: src" | ||
| } | ||
| op_kwargs: _ | ||
| dst: _ | ||
| } | ||
|
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||
| target: { | ||
| "@type": "mazepa.seq_flow" | ||
| stages: [ | ||
| #COPY_TEMPLATE & { | ||
| op_kwargs: { | ||
| src: { | ||
| "@type": "build_cv_layer" | ||
| path: #AFF_PATH | ||
| } | ||
| } | ||
| dst: { | ||
| "@type": "build_cv_layer" | ||
| path: #AFF_COPY_PATH | ||
| info_reference_path: #AFF_PATH | ||
| cv_kwargs: {"delete_black_uploads": false} | ||
| } | ||
| }, | ||
|
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||
| #COPY_TEMPLATE & { | ||
| op_kwargs: { | ||
| src: { | ||
| "@type": "build_cv_layer" | ||
| path: #BACKUP_PATH | ||
| } | ||
| } | ||
| dst: { | ||
| "@type": "build_cv_layer" | ||
| path: #BACKUP_COPY_PATH | ||
| info_reference_path: #BACKUP_PATH | ||
| cv_kwargs: {"delete_black_uploads": false} | ||
| } | ||
| }, | ||
|
|
||
| ] | ||
|
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||
| } |
85 changes: 85 additions & 0 deletions
85
specs/tommy/lee_fly_cns_segmentation_test001/230612_rework_affinities.cue
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| #AFF_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity" | ||
| #BACKUP_PATH: "gs://zetta_lee_fly_cns_001_kisuk/final/v2/affinity/backup_for_adjustments" | ||
| #ORIGINAL_BLACK_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/resin_mask_final_surgery" | ||
| #BLACK_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/resin_mask_final_surgery_consecutive3" | ||
| #SNAP_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/img_mask_stage1_v2_64nm_try_x1_iter300_rig200_lr0.001_surgery_consecutive3" | ||
| #THRESHOLD_MSK_PATH: "gs://zetta_lee_fly_cns_001_alignment_temp/aced/med_x1/try_x0/aff_mask_stage1_v2_64nm_try_x1_iter300_rig200_lr0.001_surgery" | ||
|
|
||
| "@type": "mazepa.execute_on_gcp_with_sqs" | ||
| worker_image: "us.gcr.io/zetta-lee-fly-vnc-001/zetta_utils:tmacrina_mask_affinities_x4" | ||
| worker_cluster_name: "zutils-cns" | ||
| worker_cluster_region: "us-east1" | ||
| worker_cluster_project: "zetta-lee-fly-vnc-001" | ||
| worker_resources: { | ||
| memory: "18560Mi" | ||
| } | ||
| worker_replicas: 512 | ||
| local_test: false | ||
|
|
||
| #AFF: { | ||
| "@type": "build_cv_layer" | ||
| path: #AFF_PATH | ||
| cv_kwargs: {"delete_black_uploads": false} // ws+agg require all affinities present, so cannot issue DELETES | ||
| } | ||
| #BACKUP: { | ||
| "@type": "build_cv_layer" | ||
| path: #BACKUP_PATH | ||
| info_reference_path: #AFF_PATH | ||
| } | ||
| #ORIGINAL_BLACK_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #ORIGINAL_BLACK_MSK_PATH | ||
| data_resolution: [256, 256, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
| #BLACK_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #BLACK_MSK_PATH | ||
| data_resolution: [256, 256, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
| #SNAP_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #SNAP_MSK_PATH | ||
| data_resolution: [64, 64, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
| #THRESHOLD_MASK: { | ||
| "@type": "build_cv_layer" | ||
| path: #THRESHOLD_MSK_PATH | ||
| data_resolution: [64, 64, 45] | ||
| interpolation_mode: "mask" | ||
| } | ||
|
|
||
| #BBOX: { | ||
| "@type": "BBox3D.from_coords" | ||
| start_coord: [0, 0, 0] | ||
| // end_coord: [4096, 4608, 7010] // actual | ||
| end_coord: [4176, 4752, 7020] // divisible by processing_chunk_size | ||
| resolution: [256, 256, 45] | ||
| } | ||
|
|
||
| target: { | ||
| "@type": "build_subchunkable_apply_flow" | ||
| // "@mode": "partial" | ||
| bbox: #BBOX | ||
| dst: #AFF | ||
| dst_resolution: [16, 16, 45] | ||
| processing_chunk_sizes: [[144 * 16, 144 * 16, 13]] | ||
| // must be one pixel for lowest-res mask in xy and >=1 in z for snap mask breaking | ||
| processing_crop_pads: [[16, 16, 1]] | ||
| processing_blend_pads: [[0, 0, 0]] | ||
| op: { | ||
| "@type": "ReworkAffinitiesOp" | ||
| } | ||
| op_kwargs: { | ||
| aff_layer: #AFF | ||
| aff_backup_layer: #BACKUP | ||
| original_black_mask_layer: #ORIGINAL_BLACK_MASK | ||
| black_mask_layer: #BLACK_MASK | ||
| snap_mask_layer: #SNAP_MASK | ||
| threshold_mask_layer: #THRESHOLD_MASK | ||
| threshold_value: 0.85 | ||
| fill_value: 0 | ||
| } | ||
| } |
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