Add full 3D reconstruction pipeline for LIDC-IDRI-0370
Browse files- .gitattributes +7 -0
- 01_raw_ct/LIDC-IDRI-0370_ct.nii.gz +3 -0
- 02_segmentation/LIDC-IDRI-0370_ct.nii.gz +3 -0
- 02_segmentation/LIDC-IDRI-0370_mask.nii.gz +3 -0
- 02_segmentation/LIDC-IDRI-0370_preview.png +3 -0
- 03_mesh_with_trachea/LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl +3 -0
- 04_mesh_without_trachea/LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl +3 -0
- 05_mesh_smoothed/LIDC-IDRI-0370_03_mesh_lisse_taubin.stl +3 -0
- 06_mesh_reduced/LIDC-IDRI-0370_04_mesh_qem.stl +3 -0
- 06_mesh_reduced/LIDC-IDRI-0370_lung_mesh_reduced.stl +3 -0
- 07_lung_split/LIDC-IDRI-0370_left_lung_mesh.stl +3 -0
- 07_lung_split/LIDC-IDRI-0370_right_lung_mesh.stl +3 -0
- 07_lung_split/LIDC-IDRI-0370_split_metrics.json +35 -0
- 08_fem_mesh/LIDC-IDRI-0370_fem_metrics.json +52 -0
- 08_fem_mesh/LIDC-IDRI-0370_left_lung.msh +0 -0
- 08_fem_mesh/LIDC-IDRI-0370_right_lung.msh +0 -0
- metrics/LIDC-IDRI-0370_pipeline_metrics.json +68 -0
.gitattributes
CHANGED
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@@ -58,3 +58,10 @@ 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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03_mesh_with_trachea/LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl filter=lfs diff=lfs merge=lfs -text
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04_mesh_without_trachea/LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl filter=lfs diff=lfs merge=lfs -text
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05_mesh_smoothed/LIDC-IDRI-0370_03_mesh_lisse_taubin.stl filter=lfs diff=lfs merge=lfs -text
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06_mesh_reduced/LIDC-IDRI-0370_04_mesh_qem.stl filter=lfs diff=lfs merge=lfs -text
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06_mesh_reduced/LIDC-IDRI-0370_lung_mesh_reduced.stl filter=lfs diff=lfs merge=lfs -text
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07_lung_split/LIDC-IDRI-0370_left_lung_mesh.stl filter=lfs diff=lfs merge=lfs -text
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07_lung_split/LIDC-IDRI-0370_right_lung_mesh.stl filter=lfs diff=lfs merge=lfs -text
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01_raw_ct/LIDC-IDRI-0370_ct.nii.gz
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size 118224115
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02_segmentation/LIDC-IDRI-0370_ct.nii.gz
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version https://git-lfs.github.com/spec/v1
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02_segmentation/LIDC-IDRI-0370_mask.nii.gz
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version https://git-lfs.github.com/spec/v1
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size 1114388
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02_segmentation/LIDC-IDRI-0370_preview.png
ADDED
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Git LFS Details
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03_mesh_with_trachea/LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl
ADDED
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version https://git-lfs.github.com/spec/v1
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size 43127284
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04_mesh_without_trachea/LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl
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version https://git-lfs.github.com/spec/v1
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size 37290884
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05_mesh_smoothed/LIDC-IDRI-0370_03_mesh_lisse_taubin.stl
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version https://git-lfs.github.com/spec/v1
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size 37290884
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06_mesh_reduced/LIDC-IDRI-0370_04_mesh_qem.stl
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version https://git-lfs.github.com/spec/v1
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size 3000084
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06_mesh_reduced/LIDC-IDRI-0370_lung_mesh_reduced.stl
ADDED
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version https://git-lfs.github.com/spec/v1
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size 3000084
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07_lung_split/LIDC-IDRI-0370_left_lung_mesh.stl
ADDED
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version https://git-lfs.github.com/spec/v1
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size 1466884
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07_lung_split/LIDC-IDRI-0370_right_lung_mesh.stl
ADDED
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version https://git-lfs.github.com/spec/v1
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size 1533284
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07_lung_split/LIDC-IDRI-0370_split_metrics.json
ADDED
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@@ -0,0 +1,35 @@
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{
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"patient": "LIDC-IDRI-0370",
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"mesh_source": "mesh_reduced",
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| 4 |
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"n_composantes_trouvees": 2,
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| 5 |
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"right": {
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| 6 |
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"n_vertices": 15334,
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| 7 |
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"n_faces": 30664,
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| 8 |
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"watertight": true,
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| 9 |
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"volume_mL": 2866.67,
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| 10 |
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"volume_mm3": 2866670.027,
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| 11 |
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"surface_cm2": 1297.296,
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| 12 |
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"centroide_xyz_mm": [
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160.69,
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125.73,
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| 15 |
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171.27
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],
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"taille_fichier_MB": 1.533,
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| 18 |
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"fichier_stl": "LIDC-IDRI-0370_right_lung_mesh.stl"
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| 19 |
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},
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| 20 |
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"left": {
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| 21 |
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"n_vertices": 14670,
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| 22 |
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"n_faces": 29336,
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| 23 |
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"watertight": true,
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| 24 |
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"volume_mL": 2362.625,
|
| 25 |
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"volume_mm3": 2362625.166,
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| 26 |
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"surface_cm2": 1203.011,
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| 27 |
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"centroide_xyz_mm": [
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| 28 |
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167.19,
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| 29 |
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| 31 |
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],
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"taille_fichier_MB": 1.467,
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| 33 |
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"fichier_stl": "LIDC-IDRI-0370_left_lung_mesh.stl"
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| 34 |
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}
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| 35 |
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}
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08_fem_mesh/LIDC-IDRI-0370_fem_metrics.json
ADDED
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@@ -0,0 +1,52 @@
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| 1 |
+
{
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| 2 |
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"right": {
|
| 3 |
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"label": "right",
|
| 4 |
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"n_noeuds": 8162,
|
| 5 |
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"n_tetraedres": 37937,
|
| 6 |
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"v_surfacique_mL": 2866.67,
|
| 7 |
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"v_tetraedrique_mL": 2858.497,
|
| 8 |
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"erreur_vol_pct": 0.285,
|
| 9 |
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"ok_volume": true,
|
| 10 |
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"aspect_ratio_moyen": 1.2,
|
| 11 |
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"aspect_ratio_max": 7.063,
|
| 12 |
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"pct_elements_AR_sup3": 0.06,
|
| 13 |
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"ok_aspect_ratio": true,
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| 14 |
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"n_slivers": 0,
|
| 15 |
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"pct_slivers": 0.0,
|
| 16 |
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"ok_slivers": true,
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| 17 |
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"scaled_jacobian_min": 0.12307,
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| 18 |
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"scaled_jacobian_mean": 0.4099,
|
| 19 |
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"pct_sj_inferieur_seuil": 0.13,
|
| 20 |
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"n_elements_inverses": 0,
|
| 21 |
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"ok_jacobian": true,
|
| 22 |
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"valide_fem_medical": true,
|
| 23 |
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"msh_path": "/content/reconstruction/LIDC-IDRI-0370_right_lung.msh",
|
| 24 |
+
"t_gen_s": 18.77,
|
| 25 |
+
"target_size": 7.0
|
| 26 |
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},
|
| 27 |
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"left": {
|
| 28 |
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"label": "left",
|
| 29 |
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"n_noeuds": 6567,
|
| 30 |
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"n_tetraedres": 29131,
|
| 31 |
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"v_surfacique_mL": 2362.625,
|
| 32 |
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"v_tetraedrique_mL": 2354.711,
|
| 33 |
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"erreur_vol_pct": 0.335,
|
| 34 |
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"ok_volume": true,
|
| 35 |
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"aspect_ratio_moyen": 1.21,
|
| 36 |
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"aspect_ratio_max": 3.568,
|
| 37 |
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"pct_elements_AR_sup3": 0.02,
|
| 38 |
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"ok_aspect_ratio": true,
|
| 39 |
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"n_slivers": 0,
|
| 40 |
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"pct_slivers": 0.0,
|
| 41 |
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"ok_slivers": true,
|
| 42 |
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"scaled_jacobian_min": 0.14272,
|
| 43 |
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"scaled_jacobian_mean": 0.40624,
|
| 44 |
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"pct_sj_inferieur_seuil": 0.05,
|
| 45 |
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"n_elements_inverses": 0,
|
| 46 |
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"ok_jacobian": true,
|
| 47 |
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"valide_fem_medical": true,
|
| 48 |
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"msh_path": "/content/reconstruction/LIDC-IDRI-0370_left_lung.msh",
|
| 49 |
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"t_gen_s": 7.82,
|
| 50 |
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"target_size": 7.0
|
| 51 |
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}
|
| 52 |
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}
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08_fem_mesh/LIDC-IDRI-0370_left_lung.msh
ADDED
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The diff for this file is too large to render.
See raw diff
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08_fem_mesh/LIDC-IDRI-0370_right_lung.msh
ADDED
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The diff for this file is too large to render.
See raw diff
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metrics/LIDC-IDRI-0370_pipeline_metrics.json
ADDED
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@@ -0,0 +1,68 @@
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{
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| 2 |
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"patient": "LIDC-IDRI-0370",
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| 3 |
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"voxel_spacing_mm": [
|
| 4 |
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1.0,
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1.0,
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1.0
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],
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| 8 |
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"etapes": {
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|
| 14 |
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|
| 15 |
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"fichier_stl": "LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl"
|
| 17 |
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},
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| 18 |
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"02_mesh_brut_sans_trachee": {
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| 19 |
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| 20 |
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| 23 |
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| 24 |
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|
| 25 |
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"fichier_stl": "LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl"
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| 26 |
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},
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| 27 |
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"03_mesh_lisse_taubin": {
|
| 28 |
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"n_vertices": 372912,
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| 29 |
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| 30 |
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"watertight": true,
|
| 31 |
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"volume_mL": 5229.79,
|
| 32 |
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"surface_cm2": 2499.869,
|
| 33 |
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"taille_fichier_MB": 37.291,
|
| 34 |
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"fichier_stl": "LIDC-IDRI-0370_03_mesh_lisse_taubin.stl"
|
| 35 |
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},
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| 36 |
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"04_mesh_qem": {
|
| 37 |
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"n_vertices": 30004,
|
| 38 |
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"n_faces": 60000,
|
| 39 |
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"watertight": true,
|
| 40 |
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"volume_mL": 5229.295,
|
| 41 |
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"surface_cm2": 2500.307,
|
| 42 |
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"taille_fichier_MB": 3.0,
|
| 43 |
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"fichier_stl": "LIDC-IDRI-0370_04_mesh_qem.stl",
|
| 44 |
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"hausdorff_95_sym_mm": 4.9004,
|
| 45 |
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"hausdorff_95_a2b_mm": 4.8433,
|
| 46 |
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"hausdorff_95_b2a_mm": 4.9004,
|
| 47 |
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"msd_mm": 2.4856,
|
| 48 |
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"max_dist_a2b_mm": 8.2894
|
| 49 |
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}
|
| 50 |
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},
|
| 51 |
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"reduction_qem": {
|
| 52 |
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"target_faces": 60000,
|
| 53 |
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"achieved_faces": 60000,
|
| 54 |
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"strategy": "quadric",
|
| 55 |
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"compression_ratio": 12.43,
|
| 56 |
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"temps_reduction_s": 11.985,
|
| 57 |
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"hausdorff_95_sym_mm": 4.9004,
|
| 58 |
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"msd_mm": 2.4856
|
| 59 |
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},
|
| 60 |
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"fichiers_generes": {
|
| 61 |
+
"01_avec_trachee": "LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl",
|
| 62 |
+
"02_brut_sans_trachee": "LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl",
|
| 63 |
+
"03_lisse_taubin": "LIDC-IDRI-0370_03_mesh_lisse_taubin.stl",
|
| 64 |
+
"04_qem": "LIDC-IDRI-0370_04_mesh_qem.stl",
|
| 65 |
+
"reduced_alias": "LIDC-IDRI-0370_lung_mesh_reduced.stl",
|
| 66 |
+
"metrics_json": "LIDC-IDRI-0370_pipeline_metrics.json"
|
| 67 |
+
}
|
| 68 |
+
}
|