Yousra0x0 commited on
Commit
84b1528
·
verified ·
1 Parent(s): 3cbda67

Add full 3D reconstruction pipeline for LIDC-IDRI-0370

Browse files
.gitattributes CHANGED
@@ -58,3 +58,10 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
58
  # Video files - compressed
59
  *.mp4 filter=lfs diff=lfs merge=lfs -text
60
  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
58
  # Video files - compressed
59
  *.mp4 filter=lfs diff=lfs merge=lfs -text
60
  *.webm filter=lfs diff=lfs merge=lfs -text
61
+ 03_mesh_with_trachea/LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl filter=lfs diff=lfs merge=lfs -text
62
+ 04_mesh_without_trachea/LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl filter=lfs diff=lfs merge=lfs -text
63
+ 05_mesh_smoothed/LIDC-IDRI-0370_03_mesh_lisse_taubin.stl filter=lfs diff=lfs merge=lfs -text
64
+ 06_mesh_reduced/LIDC-IDRI-0370_04_mesh_qem.stl filter=lfs diff=lfs merge=lfs -text
65
+ 06_mesh_reduced/LIDC-IDRI-0370_lung_mesh_reduced.stl filter=lfs diff=lfs merge=lfs -text
66
+ 07_lung_split/LIDC-IDRI-0370_left_lung_mesh.stl filter=lfs diff=lfs merge=lfs -text
67
+ 07_lung_split/LIDC-IDRI-0370_right_lung_mesh.stl filter=lfs diff=lfs merge=lfs -text
01_raw_ct/LIDC-IDRI-0370_ct.nii.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f3d28e76dbfa5e825f141e2904eb67459d92a23e1be48f02ff8aa285a7a9e878
3
+ size 118224115
02_segmentation/LIDC-IDRI-0370_ct.nii.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f3d28e76dbfa5e825f141e2904eb67459d92a23e1be48f02ff8aa285a7a9e878
3
+ size 118224115
02_segmentation/LIDC-IDRI-0370_mask.nii.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:64cbc30d143fe9d6ec0be3946ee513a0b7086a5ab5b848e534ca9bae667f3ba5
3
+ size 1114388
02_segmentation/LIDC-IDRI-0370_preview.png ADDED

Git LFS Details

  • SHA256: 9dc8cea275ef7647167ecd7e01522c5f6a08e06c905c522d86248a4f2722bda2
  • Pointer size: 132 Bytes
  • Size of remote file: 1.89 MB
03_mesh_with_trachea/LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:1cb68b1183459ac151042d3cb6b8cf103417de0a24cb2b91a2fb7c2677020902
3
+ size 43127284
04_mesh_without_trachea/LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2a70c05372f50c1273ce8eb3e4c461f6e37d148bc9bd1b264fbd7ed696a74764
3
+ size 37290884
05_mesh_smoothed/LIDC-IDRI-0370_03_mesh_lisse_taubin.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:eb9aa5cdf56f19982ab21b7be2bfe80dfb1f80833a4771296f1cc0bd3ed2de18
3
+ size 37290884
06_mesh_reduced/LIDC-IDRI-0370_04_mesh_qem.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:654b8627555d1ef7202d1d098639a5c805241ba46fc7e933c3c1e62bd34e1670
3
+ size 3000084
06_mesh_reduced/LIDC-IDRI-0370_lung_mesh_reduced.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:654b8627555d1ef7202d1d098639a5c805241ba46fc7e933c3c1e62bd34e1670
3
+ size 3000084
07_lung_split/LIDC-IDRI-0370_left_lung_mesh.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:65e8077f50cf0b45bdcc894a83915338902fcc82e9d326a31f64a20572d8bfdc
3
+ size 1466884
07_lung_split/LIDC-IDRI-0370_right_lung_mesh.stl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5d27755084e603921b1993d93a353dfa18accd032d4efec19179f83de5971ed1
3
+ size 1533284
07_lung_split/LIDC-IDRI-0370_split_metrics.json ADDED
@@ -0,0 +1,35 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "patient": "LIDC-IDRI-0370",
3
+ "mesh_source": "mesh_reduced",
4
+ "n_composantes_trouvees": 2,
5
+ "right": {
6
+ "n_vertices": 15334,
7
+ "n_faces": 30664,
8
+ "watertight": true,
9
+ "volume_mL": 2866.67,
10
+ "volume_mm3": 2866670.027,
11
+ "surface_cm2": 1297.296,
12
+ "centroide_xyz_mm": [
13
+ 160.69,
14
+ 125.73,
15
+ 171.27
16
+ ],
17
+ "taille_fichier_MB": 1.533,
18
+ "fichier_stl": "LIDC-IDRI-0370_right_lung_mesh.stl"
19
+ },
20
+ "left": {
21
+ "n_vertices": 14670,
22
+ "n_faces": 29336,
23
+ "watertight": true,
24
+ "volume_mL": 2362.625,
25
+ "volume_mm3": 2362625.166,
26
+ "surface_cm2": 1203.011,
27
+ "centroide_xyz_mm": [
28
+ 167.19,
29
+ 266.82,
30
+ 174.97
31
+ ],
32
+ "taille_fichier_MB": 1.467,
33
+ "fichier_stl": "LIDC-IDRI-0370_left_lung_mesh.stl"
34
+ }
35
+ }
08_fem_mesh/LIDC-IDRI-0370_fem_metrics.json ADDED
@@ -0,0 +1,52 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "right": {
3
+ "label": "right",
4
+ "n_noeuds": 8162,
5
+ "n_tetraedres": 37937,
6
+ "v_surfacique_mL": 2866.67,
7
+ "v_tetraedrique_mL": 2858.497,
8
+ "erreur_vol_pct": 0.285,
9
+ "ok_volume": true,
10
+ "aspect_ratio_moyen": 1.2,
11
+ "aspect_ratio_max": 7.063,
12
+ "pct_elements_AR_sup3": 0.06,
13
+ "ok_aspect_ratio": true,
14
+ "n_slivers": 0,
15
+ "pct_slivers": 0.0,
16
+ "ok_slivers": true,
17
+ "scaled_jacobian_min": 0.12307,
18
+ "scaled_jacobian_mean": 0.4099,
19
+ "pct_sj_inferieur_seuil": 0.13,
20
+ "n_elements_inverses": 0,
21
+ "ok_jacobian": true,
22
+ "valide_fem_medical": true,
23
+ "msh_path": "/content/reconstruction/LIDC-IDRI-0370_right_lung.msh",
24
+ "t_gen_s": 18.77,
25
+ "target_size": 7.0
26
+ },
27
+ "left": {
28
+ "label": "left",
29
+ "n_noeuds": 6567,
30
+ "n_tetraedres": 29131,
31
+ "v_surfacique_mL": 2362.625,
32
+ "v_tetraedrique_mL": 2354.711,
33
+ "erreur_vol_pct": 0.335,
34
+ "ok_volume": true,
35
+ "aspect_ratio_moyen": 1.21,
36
+ "aspect_ratio_max": 3.568,
37
+ "pct_elements_AR_sup3": 0.02,
38
+ "ok_aspect_ratio": true,
39
+ "n_slivers": 0,
40
+ "pct_slivers": 0.0,
41
+ "ok_slivers": true,
42
+ "scaled_jacobian_min": 0.14272,
43
+ "scaled_jacobian_mean": 0.40624,
44
+ "pct_sj_inferieur_seuil": 0.05,
45
+ "n_elements_inverses": 0,
46
+ "ok_jacobian": true,
47
+ "valide_fem_medical": true,
48
+ "msh_path": "/content/reconstruction/LIDC-IDRI-0370_left_lung.msh",
49
+ "t_gen_s": 7.82,
50
+ "target_size": 7.0
51
+ }
52
+ }
08_fem_mesh/LIDC-IDRI-0370_left_lung.msh ADDED
The diff for this file is too large to render. See raw diff
 
08_fem_mesh/LIDC-IDRI-0370_right_lung.msh ADDED
The diff for this file is too large to render. See raw diff
 
metrics/LIDC-IDRI-0370_pipeline_metrics.json ADDED
@@ -0,0 +1,68 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "patient": "LIDC-IDRI-0370",
3
+ "voxel_spacing_mm": [
4
+ 1.0,
5
+ 1.0,
6
+ 1.0
7
+ ],
8
+ "etapes": {
9
+ "01_mesh_brut_avec_trachee": {
10
+ "n_vertices": 431244,
11
+ "n_faces": 862544,
12
+ "watertight": true,
13
+ "volume_mL": 5450.135,
14
+ "surface_cm2": 3223.389,
15
+ "taille_fichier_MB": 43.127,
16
+ "fichier_stl": "LIDC-IDRI-0370_01_mesh_brut_avec_trachee.stl"
17
+ },
18
+ "02_mesh_brut_sans_trachee": {
19
+ "n_vertices": 372912,
20
+ "n_faces": 745816,
21
+ "watertight": true,
22
+ "volume_mL": 5241.248,
23
+ "surface_cm2": 2756.018,
24
+ "taille_fichier_MB": 37.291,
25
+ "fichier_stl": "LIDC-IDRI-0370_02_mesh_brut_sans_trachee.stl"
26
+ },
27
+ "03_mesh_lisse_taubin": {
28
+ "n_vertices": 372912,
29
+ "n_faces": 745816,
30
+ "watertight": true,
31
+ "volume_mL": 5229.79,
32
+ "surface_cm2": 2499.869,
33
+ "taille_fichier_MB": 37.291,
34
+ "fichier_stl": "LIDC-IDRI-0370_03_mesh_lisse_taubin.stl"
35
+ },
36
+ "04_mesh_qem": {
37
+ "n_vertices": 30004,
38
+ "n_faces": 60000,
39
+ "watertight": true,
40
+ "volume_mL": 5229.295,
41
+ "surface_cm2": 2500.307,
42
+ "taille_fichier_MB": 3.0,
43
+ "fichier_stl": "LIDC-IDRI-0370_04_mesh_qem.stl",
44
+ "hausdorff_95_sym_mm": 4.9004,
45
+ "hausdorff_95_a2b_mm": 4.8433,
46
+ "hausdorff_95_b2a_mm": 4.9004,
47
+ "msd_mm": 2.4856,
48
+ "max_dist_a2b_mm": 8.2894
49
+ }
50
+ },
51
+ "reduction_qem": {
52
+ "target_faces": 60000,
53
+ "achieved_faces": 60000,
54
+ "strategy": "quadric",
55
+ "compression_ratio": 12.43,
56
+ "temps_reduction_s": 11.985,
57
+ "hausdorff_95_sym_mm": 4.9004,
58
+ "msd_mm": 2.4856
59
+ },
60
+ "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
+ }