Add full yolov8 compatible post-processing (#115)

This updates the local detection to yolov8-based models from the older yolov5 based models.

This includes significant additional post-processing of the raw yolov8 output, but also means that the smaller nano yolo model is available as well as all of the updated ALVINN thorax training data.

Signed-off-by: Justin Georgi <justin.georgi@gmail.com>

Reviewed-on: Georgi_Lab/ALVINN_f7#115

src/models/thorax-0.1.0-n640/classes.json

@@ -0,0 +1,43 @@
+[
+  "Abdominal diaphragm",
+  "Aorta",
+  "Azygous vein",
+  "Brachiocephalic trunk",
+  "Caudal vena cava",
+  "Cranial vena cava",
+  "Esophagus",
+  "External abdominal oblique",
+  "Iliocostalis",
+  "Latissimus dorsi",
+  "Left atrium",
+  "Left auricle",
+  "Left lung",
+  "Left subclavian artery",
+  "Left ventricle",
+  "Longissimus",
+  "Pectoralis profundus",
+  "Pectoralis superficialis",
+  "Pericardium",
+  "Phrenic nerve",
+  "Primary bronchus",
+  "Pulmonary artery",
+  "Pulmonary trunk",
+  "Pulmonary vein",
+  "Rectus abdominis",
+  "Rectus thoracis",
+  "Recurrent laryngeal nerve",
+  "Rhomboideus",
+  "Right atrium",
+  "Right auricle",
+  "Right lung",
+  "Right ventricle",
+  "Scalenus",
+  "Serratus dorsalis caudalis",
+  "Serratus dorsalis cranialis",
+  "Serratus ventralis",
+  "Spinalis",
+  "Sympathetic chain",
+  "Trachea",
+  "Trapezius",
+  "Vagus nerve"
+]

src/models/thorax-0.1.0-n640/metadata.yaml

@@ -0,0 +1,54 @@
+description: Ultralytics thorax-0.1.0-n model trained on /data/ALVINN/Thorax/Thorax
+  0.1.0/thorax.yaml
+author: Ultralytics
+license: AGPL-3.0 https://ultralytics.com/license
+date: '2024-02-29T21:26:09.903031'
+version: 8.1.19
+stride: 32
+task: detect
+batch: 1
+imgsz:
+- 640
+- 640
+names:
+  0: Abdominal diaphragm
+  1: Aorta
+  2: Azygous vein
+  3: Brachiocephalic trunk
+  4: Caudal vena cava
+  5: Cranial vena cava
+  6: Esophagus
+  7: External abdominal oblique
+  8: Iliocostalis
+  9: Latissimus dorsi
+  10: Left atrium
+  11: Left auricle
+  12: Left lung
+  13: Left subclavian artery
+  14: Left ventricle
+  15: Longissimus
+  16: Pectoralis profundus
+  17: Pectoralis superficialis
+  18: Pericardium
+  19: Phrenic nerve
+  20: Primary bronchus
+  21: Pulmonary artery
+  22: Pulmonary trunk
+  23: Pulmonary vein
+  24: Rectus abdominis
+  25: Rectus thoracis
+  26: Recurrent laryngeal nerve
+  27: Rhomboideus
+  28: Right atrium
+  29: Right auricle
+  30: Right lung
+  31: Right ventricle
+  32: Scalenus
+  33: Serratus dorsalis caudalis
+  34: Serratus dorsalis cranialis
+  35: Serratus ventralis
+  36: Spinalis
+  37: Sympathetic chain
+  38: Trachea
+  39: Trapezius
+  40: Vagus nerve

src/models/thorax-0.1.0-n960/classes.json

@@ -0,0 +1,43 @@
+[
+  "Abdominal diaphragm",
+  "Aorta",
+  "Azygous vein",
+  "Brachiocephalic trunk",
+  "Caudal vena cava",
+  "Cranial vena cava",
+  "Esophagus",
+  "External abdominal oblique",
+  "Iliocostalis",
+  "Latissimus dorsi",
+  "Left atrium",
+  "Left auricle",
+  "Left lung",
+  "Left subclavian artery",
+  "Left ventricle",
+  "Longissimus",
+  "Pectoralis profundus",
+  "Pectoralis superficialis",
+  "Pericardium",
+  "Phrenic nerve",
+  "Primary bronchus",
+  "Pulmonary artery",
+  "Pulmonary trunk",
+  "Pulmonary vein",
+  "Rectus abdominis",
+  "Rectus thoracis",
+  "Recurrent laryngeal nerve",
+  "Rhomboideus",
+  "Right atrium",
+  "Right auricle",
+  "Right lung",
+  "Right ventricle",
+  "Scalenus",
+  "Serratus dorsalis caudalis",
+  "Serratus dorsalis cranialis",
+  "Serratus ventralis",
+  "Spinalis",
+  "Sympathetic chain",
+  "Trachea",
+  "Trapezius",
+  "Vagus nerve"
+]

src/models/thorax-0.1.0-n960/metadata.yaml

@@ -0,0 +1,53 @@
+description: Ultralytics thorax-0.1.0-n model trained on ./thorax.yaml
+author: Ultralytics
+license: AGPL-3.0 https://ultralytics.com/license
+date: '2024-02-29T23:52:02.571033'
+version: 8.1.19
+stride: 32
+task: detect
+batch: 1
+imgsz:
+- 960
+- 960
+names:
+  0: Abdominal diaphragm
+  1: Aorta
+  2: Azygous vein
+  3: Brachiocephalic trunk
+  4: Caudal vena cava
+  5: Cranial vena cava
+  6: Esophagus
+  7: External abdominal oblique
+  8: Iliocostalis
+  9: Latissimus dorsi
+  10: Left atrium
+  11: Left auricle
+  12: Left lung
+  13: Left subclavian artery
+  14: Left ventricle
+  15: Longissimus
+  16: Pectoralis profundus
+  17: Pectoralis superficialis
+  18: Pericardium
+  19: Phrenic nerve
+  20: Primary bronchus
+  21: Pulmonary artery
+  22: Pulmonary trunk
+  23: Pulmonary vein
+  24: Rectus abdominis
+  25: Rectus thoracis
+  26: Recurrent laryngeal nerve
+  27: Rhomboideus
+  28: Right atrium
+  29: Right auricle
+  30: Right lung
+  31: Right ventricle
+  32: Scalenus
+  33: Serratus dorsalis caudalis
+  34: Serratus dorsalis cranialis
+  35: Serratus ventralis
+  36: Spinalis
+  37: Sympathetic chain
+  38: Trachea
+  39: Trapezius
+  40: Vagus nerve

src/models/thorax_tfwm/classes.json

@@ -1,12 +0,0 @@
-[
-  "Right lung",
-  "Diaphragm",
-  "Heart",
-  "Caudal vena cava",
-  "Cranial vena cava",
-  "Phrenic nerve",
-  "Trachea",
-  "Vagus nerve",
-  "Left Lung",
-  "Aorta"
-]