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- .gitattributes +4 -0
- production_iteration_state/2026-08-03/README.md +17 -0
- production_iteration_state/2026-08-03/harvest_sweep/cubes.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w0/block.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w0/block_l0.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w0/instances.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w0/labels_on_ours.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/pred_fwd.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/pred_rev.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/prob/blk.json +7 -0
- production_iteration_state/2026-08-03/mosaic/w0/prob/blk.pkl +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/prob/blk.tif +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/prob/dataset.json +12 -0
- production_iteration_state/2026-08-03/mosaic/w0/prob/plans.json +346 -0
- production_iteration_state/2026-08-03/mosaic/w0/prob/predict_from_raw_data_args.json +15 -0
- production_iteration_state/2026-08-03/mosaic/w0/surface_valid.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/surface_xyz_l1.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w0/winding.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w1/block.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w1/block_l0.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w1/instances.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w1/labels_on_ours.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/pred_fwd.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/pred_rev.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/prob/blk.json +7 -0
- production_iteration_state/2026-08-03/mosaic/w1/prob/blk.pkl +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/prob/blk.tif +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/prob/dataset.json +12 -0
- production_iteration_state/2026-08-03/mosaic/w1/prob/plans.json +346 -0
- production_iteration_state/2026-08-03/mosaic/w1/prob/predict_from_raw_data_args.json +15 -0
- production_iteration_state/2026-08-03/mosaic/w1/surface_valid.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/surface_xyz_l1.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w1/winding.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w2/block.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w2/block_l0.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w2/instances.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w2/labels_on_ours.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/pred_fwd.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/pred_rev.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/prob/blk.json +7 -0
- production_iteration_state/2026-08-03/mosaic/w2/prob/blk.pkl +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/prob/blk.tif +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/prob/dataset.json +12 -0
- production_iteration_state/2026-08-03/mosaic/w2/prob/plans.json +346 -0
- production_iteration_state/2026-08-03/mosaic/w2/prob/predict_from_raw_data_args.json +15 -0
- production_iteration_state/2026-08-03/mosaic/w2/surface_valid.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/surface_xyz_l1.npy +3 -0
- production_iteration_state/2026-08-03/mosaic/w2/winding.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w3/block.json +1 -0
- production_iteration_state/2026-08-03/mosaic/w3/block_l0.json +1 -0
.gitattributes
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@@ -58,3 +58,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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production_iteration_state/2026-08-03/mosaic/w0/prob/blk.tif filter=lfs diff=lfs merge=lfs -text
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production_iteration_state/2026-08-03/mosaic/w1/prob/blk.tif filter=lfs diff=lfs merge=lfs -text
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production_iteration_state/2026-08-03/mosaic/w2/prob/blk.tif filter=lfs diff=lfs merge=lfs -text
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production_iteration_state/2026-08-03/mosaic/w3/prob/blk.tif filter=lfs diff=lfs merge=lfs -text
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production_iteration_state/2026-08-03/README.md
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# production_iteration server state — 2026-08-03 checkpoint
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Derived state that is expensive to recompute; everything else refetches from S3/HF on
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demand (see production_iteration/RESUME_HERE.md for the cold rebuild).
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Restore: download this folder to /workspace/pi/ (folder names match working paths), then
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zstd -d p1447/instances.npy.zst -o /workspace/pi/p1447/instances.npy
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- mosaic/w{0..3}/ — 1667 mosaic rehearsal (pooled v3 AUC 0.845): fitted surfaces,
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pred_{fwd,rev}.npy, labels_on_ours.npy, winding.json per window. Needed for the
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geometric-recto-rule validation (next step). Recompute cost ~3 h GPU.
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- p1447/ — PHerc1447 certified instances (zstd, 13.5 GiB raw) + fitted 62.9 mm^2
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surface at the contrast-328 core. ct.npy/m7.npy NOT included (deterministic S3 refetch,
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box.json has the bbox). Recompute cost ~1 h.
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- patch/, patch_ink5/ — superseded 1667 v1/v3 single-window surfaces + label maps (kept
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small files only; baselines for regression checks).
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- harvest_sweep/cubes.json — sweep cube centres (patch_extract.best_region_centre input).
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production_iteration_state/2026-08-03/harvest_sweep/cubes.json
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[{"i": 0, "centre_l1": [4805.94873046875, 3728.77978515625, 1918.6817626953125], "origin_l1": [4647, 3570, 1760], "material": 0.9999937529455725}, {"i": 1, "centre_l1": [4534.92041015625, 2775.08203125, 2117.833251953125], "origin_l1": [4376, 2617, 1959], "material": 0.9999932506698396}, {"i": 2, "centre_l1": [13382.5830078125, 3784.3916015625, 2276.3720703125], "origin_l1": [13224, 3626, 2118], "material": 0.9999970805223027}, {"i": 3, "centre_l1": [14044.5615234375, 4571.25390625, 2390.145751953125], "origin_l1": [13886, 4413, 2232], "material": 0.9999873803222118}, {"i": 4, "centre_l1": [15250.4912109375, 3968.376953125, 2537.91943359375], "origin_l1": [15092, 3810, 2379], "material": 0.999998964056301}, {"i": 5, "centre_l1": [7119.8564453125, 1825.0557861328125, 2644.8310546875], "origin_l1": [6961, 1667, 2486], "material": 0.9999453461218176}, {"i": 6, "centre_l1": [12324.0634765625, 2891.744384765625, 2803.730224609375], "origin_l1": [12166, 2733, 2645], "material": 0.9999985873495013}, {"i": 7, "centre_l1": [11800.7158203125, 4831.3857421875, 2948.501708984375], "origin_l1": [11642, 4673, 2790], "material": 0.9999935645921727}, {"i": 8, "centre_l1": [9704.1689453125, 4793.224609375, 3116.8603515625], "origin_l1": [9546, 4635, 2958], "material": 0.9999848689435474}, {"i": 9, "centre_l1": [6830.6279296875, 2007.1893310546875, 3342.939697265625], "origin_l1": [6672, 1849, 3184], "material": 0.9999818552891503}, {"i": 10, "centre_l1": [4475.7041015625, 4939.33642578125, 3467.32763671875], "origin_l1": [4317, 4781, 3309], "material": 0.9997799404445386}, {"i": 11, "centre_l1": [12859.7119140625, 2447.78662109375, 3658.1162109375], "origin_l1": [12701, 2289, 3500], "material": 0.9999994663320338}, {"i": 12, "centre_l1": [6671.71630859375, 2790.746826171875, 3741.066162109375], "origin_l1": [6513, 2632, 3583], "material": 0.9999976141902689}, {"i": 13, "centre_l1": [18113.236328125, 4702.79931640625, 3893.104248046875], "origin_l1": [17955, 4544, 3735], "material": 0.8184250623284944}, {"i": 14, "centre_l1": [1716.515380859375, 1936.182861328125, 4072.421142578125], "origin_l1": [1558, 1778, 3914], "material": 0.9999678229608633}, {"i": 15, "centre_l1": [11320.994140625, 5014.43310546875, 4177.244140625], "origin_l1": [11162, 4856, 4019], "material": 0.9999954795184042}, {"i": 16, "centre_l1": [5651.83251953125, 3615.63330078125, 4302.1201171875], "origin_l1": [5493, 3457, 4144], "material": 0.9999990582330008}, {"i": 17, "centre_l1": [4059.849853515625, 4260.359375, 4433.27099609375], "origin_l1": [3901, 4102, 4275], "material": 0.999999277978634}, {"i": 18, "centre_l1": [14078.392578125, 2515.527587890625, 4597.21142578125], "origin_l1": [13920, 2357, 4439], "material": 0.999997833935902}, {"i": 19, "centre_l1": [11342.4013671875, 3029.1162109375, 4878.42333984375], "origin_l1": [11184, 2871, 4720], "material": 0.9999901114465092}, {"i": 20, "centre_l1": [2882.114013671875, 3037.9794921875, 4952.099609375], "origin_l1": [2724, 2879, 4794], "material": 0.999987913990178}, {"i": 21, "centre_l1": [13525.0205078125, 2959.721923828125, 5338.05322265625], "origin_l1": [13367, 2801, 5180], "material": 0.9999832993318822}, {"i": 22, "centre_l1": [15309.2763671875, 3523.7841796875, 5573.0166015625], "origin_l1": [15151, 3365, 5415], "material": 0.9999923089028405}, {"i": 23, "centre_l1": [16475.234375, 3963.356201171875, 5668.876953125], "origin_l1": [16317, 3805, 5510], "material": 0.9999498979956467}]
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production_iteration_state/2026-08-03/mosaic/w0/block.json
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{"origin_l1": [11648, 4352, 2560]}
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{"origin": [25728, 9600, 6272]}
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production_iteration_state/2026-08-03/mosaic/w0/instances.json
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{"1": {"tile": [0, 0, 0], "vox": 50350, "moat": 0.82}, "2": {"tile": [0, 0, 0], "vox": 139418, "moat": 0.64}, "3": {"tile": [0, 0, 0], "vox": 98726, "moat": 0.66}, "4": {"tile": [0, 0, 192], "vox": 266730, "moat": 0.74}, "5": {"tile": [0, 0, 192], "vox": 190184, "moat": 0.82}, "6": {"tile": [0, 0, 192], "vox": 98300, "moat": 0.87}, "7": {"tile": [0, 0, 192], "vox": 79031, "moat": 0.82}, "8": {"tile": [0, 0, 192], "vox": 62415, "moat": 0.78}, "9": {"tile": [0, 0, 192], "vox": 106094, "moat": 0.74}, "10": {"tile": [0, 0, 384], "vox": 202861, "moat": 0.84}, "11": {"tile": [0, 0, 384], "vox": 51112, "moat": 0.78}, "12": {"tile": [0, 0, 384], "vox": 54482, "moat": 0.84}, "13": {"tile": [0, 0, 384], "vox": 243820, "moat": 0.74}, "14": {"tile": [0, 0, 384], "vox": 212657, "moat": 0.8}, "15": {"tile": [0, 0, 384], "vox": 105646, "moat": 0.93}, "16": {"tile": [0, 0, 384], "vox": 79102, "moat": 0.86}, "17": {"tile": [0, 0, 576], "vox": 129945, "moat": 0.91}, "18": {"tile": [0, 0, 576], "vox": 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|
production_iteration_state/2026-08-03/mosaic/w0/labels_on_ours.npy
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:180edd94b6927c8a28e9ab88bbac0dfd203d96ada6437c9733ea9b776bb83d09
|
| 3 |
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size 1530865
|
production_iteration_state/2026-08-03/mosaic/w0/pred_fwd.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 6123076
|
production_iteration_state/2026-08-03/mosaic/w0/pred_rev.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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| 3 |
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size 6123076
|
production_iteration_state/2026-08-03/mosaic/w0/prob/blk.json
ADDED
|
@@ -0,0 +1,7 @@
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+
{
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+
"spacing": [
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| 4 |
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| 5 |
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|
| 6 |
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|
| 7 |
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|
production_iteration_state/2026-08-03/mosaic/w0/prob/blk.pkl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 3 |
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size 181
|
production_iteration_state/2026-08-03/mosaic/w0/prob/blk.tif
ADDED
|
|
Git LFS Details
|
production_iteration_state/2026-08-03/mosaic/w0/prob/dataset.json
ADDED
|
@@ -0,0 +1,12 @@
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| 1 |
+
{
|
| 2 |
+
"channel_names": {
|
| 3 |
+
"0": "CT"
|
| 4 |
+
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|
| 5 |
+
"labels": {
|
| 6 |
+
"background": 0,
|
| 7 |
+
"fiber": 1
|
| 8 |
+
},
|
| 9 |
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"numTraining": 1754,
|
| 10 |
+
"file_ending": ".tif",
|
| 11 |
+
"overwrite_image_reader_writer": "Tiff3DIO"
|
| 12 |
+
}
|
production_iteration_state/2026-08-03/mosaic/w0/prob/plans.json
ADDED
|
@@ -0,0 +1,346 @@
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|
| 1 |
+
{
|
| 2 |
+
"dataset_name": "Dataset059_s1_s4_s5_patches_frangiedt",
|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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1.0,
|
| 7 |
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|
| 8 |
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],
|
| 9 |
+
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|
| 10 |
+
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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0,
|
| 17 |
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|
| 18 |
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|
| 19 |
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],
|
| 20 |
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|
| 21 |
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0,
|
| 22 |
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|
| 23 |
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|
| 24 |
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],
|
| 25 |
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"configurations": {
|
| 26 |
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|
| 27 |
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"data_identifier": "nnUNetPlans_2d",
|
| 28 |
+
"preprocessor_name": "DefaultPreprocessor",
|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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|
| 38 |
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|
| 39 |
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|
| 40 |
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|
| 41 |
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|
| 42 |
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|
| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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false
|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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|
| 72 |
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|
| 73 |
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|
| 74 |
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|
| 75 |
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|
| 76 |
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|
| 77 |
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|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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|
| 82 |
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|
| 83 |
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|
| 84 |
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| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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|
| 97 |
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|
| 98 |
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|
| 99 |
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|
| 100 |
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|
| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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| 109 |
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|
| 117 |
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|
| 121 |
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| 123 |
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|
| 124 |
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|
| 125 |
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|
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|
| 129 |
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|
| 130 |
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| 131 |
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| 132 |
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|
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| 134 |
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|
| 142 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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},
|
| 155 |
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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}
|
| 161 |
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|
| 162 |
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|
| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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|
| 167 |
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]
|
| 168 |
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},
|
| 169 |
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|
| 170 |
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},
|
| 171 |
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|
| 172 |
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"data_identifier": "nnUNetPlans_3d_fullres",
|
| 173 |
+
"preprocessor_name": "DefaultPreprocessor",
|
| 174 |
+
"distance_maps_dir": "/opt/dlami/nvme/nnUNet_preprocessed/Dataset059_s1_s4_s5_patches_frangiedt/nnUNetPlans_3d_fullres/",
|
| 175 |
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|
| 176 |
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|
| 177 |
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|
| 178 |
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|
| 179 |
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192
|
| 180 |
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],
|
| 181 |
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|
| 182 |
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| 183 |
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| 184 |
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|
| 185 |
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],
|
| 186 |
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| 187 |
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| 188 |
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| 189 |
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| 190 |
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|
| 191 |
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|
| 192 |
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"CTNormalization"
|
| 193 |
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],
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| 194 |
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"use_mask_for_norm": [
|
| 195 |
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false
|
| 196 |
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],
|
| 197 |
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|
| 198 |
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|
| 199 |
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|
| 200 |
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|
| 201 |
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|
| 202 |
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|
| 203 |
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| 204 |
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},
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| 205 |
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|
| 206 |
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|
| 207 |
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|
| 208 |
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|
| 209 |
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|
| 210 |
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},
|
| 211 |
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| 212 |
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|
| 213 |
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|
| 214 |
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|
| 215 |
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|
| 216 |
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|
| 217 |
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},
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| 218 |
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|
| 219 |
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"network_class_name": "dynamic_network_architectures.architectures.unet.ResidualEncoderUNet",
|
| 220 |
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|
| 221 |
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|
| 222 |
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|
| 223 |
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|
| 225 |
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| 226 |
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|
| 227 |
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|
| 228 |
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|
| 229 |
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| 230 |
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|
| 231 |
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| 232 |
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| 234 |
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|
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|
| 311 |
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|
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|
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|
| 320 |
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|
| 321 |
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|
| 322 |
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|
| 323 |
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|
| 324 |
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|
| 325 |
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|
| 326 |
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|
| 327 |
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|
| 328 |
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|
| 329 |
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|
| 330 |
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|
| 331 |
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}
|
| 332 |
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},
|
| 333 |
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|
| 334 |
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|
| 335 |
+
"foreground_intensity_properties_per_channel": {
|
| 336 |
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"0": {
|
| 337 |
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"max": 255.0,
|
| 338 |
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|
| 339 |
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|
| 340 |
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|
| 341 |
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|
| 342 |
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|
| 343 |
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"std": 42.188316345214844
|
| 344 |
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}
|
| 345 |
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}
|
| 346 |
+
}
|
production_iteration_state/2026-08-03/mosaic/w0/prob/predict_from_raw_data_args.json
ADDED
|
@@ -0,0 +1,15 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
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|
| 3 |
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|
| 4 |
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[
|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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| 12 |
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| 14 |
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|
| 15 |
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|
production_iteration_state/2026-08-03/mosaic/w0/surface_valid.npy
ADDED
|
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|
production_iteration_state/2026-08-03/mosaic/w0/surface_xyz_l1.npy
ADDED
|
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production_iteration_state/2026-08-03/mosaic/w0/winding.json
ADDED
|
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|
|
| 1 |
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{"grid_seed": [1448, 3608], "grid_r": 89}
|
production_iteration_state/2026-08-03/mosaic/w1/block.json
ADDED
|
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|
|
| 1 |
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{"origin_l1": [3200, 1920, 3968]}
|
production_iteration_state/2026-08-03/mosaic/w1/block_l0.json
ADDED
|
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|
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{"origin": [7552, 3712, 8576]}
|
production_iteration_state/2026-08-03/mosaic/w1/instances.json
ADDED
|
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production_iteration_state/2026-08-03/mosaic/w1/labels_on_ours.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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| 3 |
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size 6230418
|
production_iteration_state/2026-08-03/mosaic/w1/pred_fwd.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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|
production_iteration_state/2026-08-03/mosaic/w1/pred_rev.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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|
production_iteration_state/2026-08-03/mosaic/w1/prob/blk.json
ADDED
|
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| 1 |
+
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|
| 2 |
+
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| 3 |
+
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|
| 4 |
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|
| 5 |
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|
| 6 |
+
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|
| 7 |
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|
production_iteration_state/2026-08-03/mosaic/w1/prob/blk.pkl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 181
|
production_iteration_state/2026-08-03/mosaic/w1/prob/blk.tif
ADDED
|
|
Git LFS Details
|
production_iteration_state/2026-08-03/mosaic/w1/prob/dataset.json
ADDED
|
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| 1 |
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{
|
| 2 |
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"channel_names": {
|
| 3 |
+
"0": "CT"
|
| 4 |
+
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|
| 5 |
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"labels": {
|
| 6 |
+
"background": 0,
|
| 7 |
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| 8 |
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|
| 9 |
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|
| 10 |
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"file_ending": ".tif",
|
| 11 |
+
"overwrite_image_reader_writer": "Tiff3DIO"
|
| 12 |
+
}
|
production_iteration_state/2026-08-03/mosaic/w1/prob/plans.json
ADDED
|
@@ -0,0 +1,346 @@
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|
| 1 |
+
{
|
| 2 |
+
"dataset_name": "Dataset059_s1_s4_s5_patches_frangiedt",
|
| 3 |
+
"plans_name": "nnUNetResEncUNetPlans_40G",
|
| 4 |
+
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|
| 5 |
+
1.0,
|
| 6 |
+
1.0,
|
| 7 |
+
1.0
|
| 8 |
+
],
|
| 9 |
+
"original_median_shape_after_transp": [
|
| 10 |
+
172,
|
| 11 |
+
172,
|
| 12 |
+
172
|
| 13 |
+
],
|
| 14 |
+
"image_reader_writer": "Tiff3DIO",
|
| 15 |
+
"transpose_forward": [
|
| 16 |
+
0,
|
| 17 |
+
1,
|
| 18 |
+
2
|
| 19 |
+
],
|
| 20 |
+
"transpose_backward": [
|
| 21 |
+
0,
|
| 22 |
+
1,
|
| 23 |
+
2
|
| 24 |
+
],
|
| 25 |
+
"configurations": {
|
| 26 |
+
"2d": {
|
| 27 |
+
"data_identifier": "nnUNetPlans_2d",
|
| 28 |
+
"preprocessor_name": "DefaultPreprocessor",
|
| 29 |
+
"batch_size": 420,
|
| 30 |
+
"patch_size": [
|
| 31 |
+
192,
|
| 32 |
+
192
|
| 33 |
+
],
|
| 34 |
+
"median_image_size_in_voxels": [
|
| 35 |
+
172.0,
|
| 36 |
+
172.0
|
| 37 |
+
],
|
| 38 |
+
"spacing": [
|
| 39 |
+
1.0,
|
| 40 |
+
1.0
|
| 41 |
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],
|
| 42 |
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|
| 43 |
+
"CTNormalization"
|
| 44 |
+
],
|
| 45 |
+
"use_mask_for_norm": [
|
| 46 |
+
false
|
| 47 |
+
],
|
| 48 |
+
"resampling_fn_data": "resample_data_or_seg_to_shape",
|
| 49 |
+
"resampling_fn_seg": "resample_data_or_seg_to_shape",
|
| 50 |
+
"resampling_fn_data_kwargs": {
|
| 51 |
+
"is_seg": false,
|
| 52 |
+
"order": 3,
|
| 53 |
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|
| 54 |
+
"force_separate_z": null
|
| 55 |
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},
|
| 56 |
+
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|
| 57 |
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"is_seg": true,
|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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},
|
| 62 |
+
"resampling_fn_probabilities": "resample_data_or_seg_to_shape",
|
| 63 |
+
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|
| 64 |
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"is_seg": false,
|
| 65 |
+
"order": 1,
|
| 66 |
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|
| 67 |
+
"force_separate_z": null
|
| 68 |
+
},
|
| 69 |
+
"architecture": {
|
| 70 |
+
"network_class_name": "dynamic_network_architectures.architectures.unet.ResidualEncoderUNet",
|
| 71 |
+
"arch_kwargs": {
|
| 72 |
+
"n_stages": 6,
|
| 73 |
+
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|
| 74 |
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32,
|
| 75 |
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64,
|
| 76 |
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128,
|
| 77 |
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256,
|
| 78 |
+
512,
|
| 79 |
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512
|
| 80 |
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],
|
| 81 |
+
"conv_op": "torch.nn.modules.conv.Conv2d",
|
| 82 |
+
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|
| 83 |
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[
|
| 84 |
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3,
|
| 85 |
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3
|
| 86 |
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],
|
| 87 |
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[
|
| 88 |
+
3,
|
| 89 |
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3
|
| 90 |
+
],
|
| 91 |
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[
|
| 92 |
+
3,
|
| 93 |
+
3
|
| 94 |
+
],
|
| 95 |
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[
|
| 96 |
+
3,
|
| 97 |
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3
|
| 98 |
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],
|
| 99 |
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[
|
| 100 |
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3,
|
| 101 |
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3
|
| 102 |
+
],
|
| 103 |
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[
|
| 104 |
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3,
|
| 105 |
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3
|
| 106 |
+
]
|
| 107 |
+
],
|
| 108 |
+
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|
| 109 |
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[
|
| 110 |
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1,
|
| 111 |
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1
|
| 112 |
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],
|
| 113 |
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[
|
| 114 |
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2,
|
| 115 |
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2
|
| 116 |
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],
|
| 117 |
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|
| 118 |
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2,
|
| 119 |
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2
|
| 120 |
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|
| 121 |
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|
| 122 |
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2,
|
| 123 |
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2
|
| 124 |
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|
| 125 |
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|
| 126 |
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2,
|
| 127 |
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2
|
| 128 |
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|
| 129 |
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|
| 130 |
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2,
|
| 131 |
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2
|
| 132 |
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]
|
| 133 |
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],
|
| 134 |
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|
| 135 |
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1,
|
| 136 |
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|
| 137 |
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4,
|
| 138 |
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6,
|
| 139 |
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6,
|
| 140 |
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6
|
| 141 |
+
],
|
| 142 |
+
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|
| 143 |
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1,
|
| 144 |
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1,
|
| 145 |
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1,
|
| 146 |
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1,
|
| 147 |
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1
|
| 148 |
+
],
|
| 149 |
+
"conv_bias": true,
|
| 150 |
+
"norm_op": "torch.nn.modules.instancenorm.InstanceNorm2d",
|
| 151 |
+
"norm_op_kwargs": {
|
| 152 |
+
"eps": 1e-05,
|
| 153 |
+
"affine": true
|
| 154 |
+
},
|
| 155 |
+
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|
| 156 |
+
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|
| 157 |
+
"nonlin": "torch.nn.LeakyReLU",
|
| 158 |
+
"nonlin_kwargs": {
|
| 159 |
+
"inplace": true
|
| 160 |
+
}
|
| 161 |
+
},
|
| 162 |
+
"_kw_requires_import": [
|
| 163 |
+
"conv_op",
|
| 164 |
+
"norm_op",
|
| 165 |
+
"dropout_op",
|
| 166 |
+
"nonlin"
|
| 167 |
+
]
|
| 168 |
+
},
|
| 169 |
+
"batch_dice": true
|
| 170 |
+
},
|
| 171 |
+
"3d_fullres": {
|
| 172 |
+
"data_identifier": "nnUNetPlans_3d_fullres",
|
| 173 |
+
"preprocessor_name": "DefaultPreprocessor",
|
| 174 |
+
"distance_maps_dir": "/opt/dlami/nvme/nnUNet_preprocessed/Dataset059_s1_s4_s5_patches_frangiedt/nnUNetPlans_3d_fullres/",
|
| 175 |
+
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|
| 176 |
+
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|
| 177 |
+
192,
|
| 178 |
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192,
|
| 179 |
+
192
|
| 180 |
+
],
|
| 181 |
+
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|
| 182 |
+
172.0,
|
| 183 |
+
172.0,
|
| 184 |
+
172.0
|
| 185 |
+
],
|
| 186 |
+
"spacing": [
|
| 187 |
+
1.0,
|
| 188 |
+
1.0,
|
| 189 |
+
1.0
|
| 190 |
+
],
|
| 191 |
+
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|
| 192 |
+
"CTNormalization"
|
| 193 |
+
],
|
| 194 |
+
"use_mask_for_norm": [
|
| 195 |
+
false
|
| 196 |
+
],
|
| 197 |
+
"resampling_fn_data": "resample_data_or_seg_to_shape",
|
| 198 |
+
"resampling_fn_seg": "resample_data_or_seg_to_shape",
|
| 199 |
+
"resampling_fn_data_kwargs": {
|
| 200 |
+
"is_seg": false,
|
| 201 |
+
"order": 3,
|
| 202 |
+
"order_z": 0,
|
| 203 |
+
"force_separate_z": null
|
| 204 |
+
},
|
| 205 |
+
"resampling_fn_seg_kwargs": {
|
| 206 |
+
"is_seg": true,
|
| 207 |
+
"order": 1,
|
| 208 |
+
"order_z": 0,
|
| 209 |
+
"force_separate_z": null
|
| 210 |
+
},
|
| 211 |
+
"resampling_fn_probabilities": "resample_data_or_seg_to_shape",
|
| 212 |
+
"resampling_fn_probabilities_kwargs": {
|
| 213 |
+
"is_seg": false,
|
| 214 |
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"order": 1,
|
| 215 |
+
"order_z": 0,
|
| 216 |
+
"force_separate_z": null
|
| 217 |
+
},
|
| 218 |
+
"architecture": {
|
| 219 |
+
"network_class_name": "dynamic_network_architectures.architectures.unet.ResidualEncoderUNet",
|
| 220 |
+
"arch_kwargs": {
|
| 221 |
+
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|
| 222 |
+
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|
| 223 |
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32,
|
| 224 |
+
64,
|
| 225 |
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128,
|
| 226 |
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256,
|
| 227 |
+
320,
|
| 228 |
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320
|
| 229 |
+
],
|
| 230 |
+
"conv_op": "torch.nn.modules.conv.Conv3d",
|
| 231 |
+
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|
| 232 |
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[
|
| 233 |
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3,
|
| 234 |
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3,
|
| 235 |
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3
|
| 236 |
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],
|
| 237 |
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|
| 238 |
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| 239 |
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3,
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| 240 |
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| 241 |
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| 242 |
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| 243 |
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3,
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| 244 |
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| 245 |
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| 246 |
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| 247 |
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| 252 |
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| 257 |
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3,
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| 294 |
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1,
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| 308 |
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| 309 |
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|
| 310 |
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|
| 311 |
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|
| 312 |
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|
| 313 |
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|
| 314 |
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|
| 315 |
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|
| 316 |
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|
| 317 |
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|
| 318 |
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"nonlin": "torch.nn.LeakyReLU",
|
| 319 |
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|
| 320 |
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|
| 321 |
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|
| 322 |
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|
| 323 |
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"_kw_requires_import": [
|
| 324 |
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"conv_op",
|
| 325 |
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|
| 326 |
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|
| 327 |
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"nonlin"
|
| 328 |
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|
| 329 |
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|
| 330 |
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|
| 331 |
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|
| 332 |
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|
| 333 |
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|
| 334 |
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|
| 335 |
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|
| 336 |
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| 337 |
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|
| 338 |
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|
| 341 |
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| 343 |
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| 344 |
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| 345 |
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| 346 |
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|
production_iteration_state/2026-08-03/mosaic/w1/prob/predict_from_raw_data_args.json
ADDED
|
@@ -0,0 +1,15 @@
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|
| 1 |
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{
|
| 2 |
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|
| 3 |
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|
| 4 |
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[
|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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"save_probabilities": true
|
| 15 |
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production_iteration_state/2026-08-03/mosaic/w1/surface_valid.npy
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
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| 3 |
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size 11195
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production_iteration_state/2026-08-03/mosaic/w1/surface_xyz_l1.npy
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 265736
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production_iteration_state/2026-08-03/mosaic/w1/winding.json
ADDED
|
@@ -0,0 +1 @@
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|
| 1 |
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{"grid_seed": [445, 473], "grid_r": 89}
|
production_iteration_state/2026-08-03/mosaic/w2/block.json
ADDED
|
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{"origin_l1": [11648, 4608, 2432]}
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production_iteration_state/2026-08-03/mosaic/w2/block_l0.json
ADDED
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production_iteration_state/2026-08-03/mosaic/w2/instances.json
ADDED
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|
production_iteration_state/2026-08-03/mosaic/w2/labels_on_ours.npy
ADDED
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| 1 |
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version https://git-lfs.github.com/spec/v1
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| 3 |
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size 19576873
|
production_iteration_state/2026-08-03/mosaic/w2/pred_fwd.npy
ADDED
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@@ -0,0 +1,3 @@
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production_iteration_state/2026-08-03/mosaic/w2/pred_rev.npy
ADDED
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version https://git-lfs.github.com/spec/v1
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| 3 |
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size 78307108
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production_iteration_state/2026-08-03/mosaic/w2/prob/blk.json
ADDED
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| 1 |
+
{
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| 2 |
+
"spacing": [
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| 3 |
+
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| 4 |
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|
| 5 |
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| 6 |
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|
| 7 |
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|
production_iteration_state/2026-08-03/mosaic/w2/prob/blk.pkl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
version https://git-lfs.github.com/spec/v1
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size 181
|
production_iteration_state/2026-08-03/mosaic/w2/prob/blk.tif
ADDED
|
|
Git LFS Details
|
production_iteration_state/2026-08-03/mosaic/w2/prob/dataset.json
ADDED
|
@@ -0,0 +1,12 @@
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| 1 |
+
{
|
| 2 |
+
"channel_names": {
|
| 3 |
+
"0": "CT"
|
| 4 |
+
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|
| 5 |
+
"labels": {
|
| 6 |
+
"background": 0,
|
| 7 |
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"fiber": 1
|
| 8 |
+
},
|
| 9 |
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"numTraining": 1754,
|
| 10 |
+
"file_ending": ".tif",
|
| 11 |
+
"overwrite_image_reader_writer": "Tiff3DIO"
|
| 12 |
+
}
|
production_iteration_state/2026-08-03/mosaic/w2/prob/plans.json
ADDED
|
@@ -0,0 +1,346 @@
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|
|
|
| 1 |
+
{
|
| 2 |
+
"dataset_name": "Dataset059_s1_s4_s5_patches_frangiedt",
|
| 3 |
+
"plans_name": "nnUNetResEncUNetPlans_40G",
|
| 4 |
+
"original_median_spacing_after_transp": [
|
| 5 |
+
1.0,
|
| 6 |
+
1.0,
|
| 7 |
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