Merge pull request #89 from Hendrik-code/tanja

Added vibe instances

Author: TanjaLe

TPTBox/core/poi.py

@@ -1247,3 +1247,16 @@ def calc_poi_average(pois: list[POI], keep_points_not_present_in_all_pois: bool
     # Sort the new ctd by keys
     ctd = dict(sorted(ctd.items()))
     return POI(centroids=ctd, orientation=pois[0].orientation, zoom=pois[0].zoom, shape=pois[0].shape, rotation=pois[0].rotation)
+
+
+def _load_from_POI_spine_r(data: dict):
+    orientation = None
+    centroids = POI_Descriptor()
+    for d in data["centroids"]["centroids"]:
+        if "direction" in d:
+            orientation = d["direction"]
+            continue
+        centroids[d["label"], 50] = (d["X"], d["Y"], d["Z"])
+    zoom = data["Spacing"]
+    shape = data["Shape"]
+    return POI(centroids, orientation=orientation, zoom=zoom, shape=shape, info=data, rotation=None)  # type: ignore

TPTBox/core/poi_fun/poi_global.py

@@ -69,6 +69,12 @@ def zoom(self):
     def origin(self):
         return (0, 0, 0)
 
+    @property
+    def orientation(self):
+        if self.itk_coords:
+            return ("L", "A", "S")
+        return ("R", "P", "S")
+
     @property
     def is_global(self) -> bool:
         """

TPTBox/core/vert_constants.py

@@ -140,6 +140,81 @@ def _get_id(cls, s: str | int, no_raise=True) -> int:  # noqa: ARG003
         return int(s)
 
 
+class Full_Body_Instance_Vibe(Abstract_lvl):
+    spleen = 1
+    kidney_right = 2
+    kidney_left = 3
+    gallbladder = 4
+    liver = 5
+    stomach = 6
+    pancreas = 7
+    adrenal_gland_right = 8
+    adrenal_gland_left = 9
+    lung_upper_lobe_left = 10
+    lung_lower_lobe_left = 11
+    lung_upper_lobe_right = 12
+    lung_middle_lobe_right = 13
+    lung_lower_lobe_right = 14
+    esophagus = 15
+    trachea = 16
+    thyroid_gland = 17
+    intestine = 18
+    duodenum = 19
+    unused = 20
+    urinary_bladder = 21
+    prostate = 22
+    sacrum = 23
+    heart = 24
+    aorta = 25
+    pulmonary_vein = 26
+    brachiocephalic_trunk = 27
+    subclavian_artery_right = 28
+    subclavian_artery_left = 29
+    common_carotid_artery_right = 30
+    common_carotid_artery_left = 31
+    brachiocephalic_vein_left = 32
+    brachiocephalic_vein_right = 33
+    atrial_appendage_left = 34
+    superior_vena_cava = 35
+    inferior_vena_cava = 36
+    portal_vein_and_splenic_vein = 37
+    iliac_artery_left = 38
+    iliac_artery_right = 39
+    iliac_vena_left = 40
+    iliac_vena_right = 41
+    humerus_left = 42
+    humerus_right = 43
+    scapula_left = 44
+    scapula_right = 45
+    clavicula_left = 46
+    clavicula_right = 47
+    femur_left = 48
+    femur_right = 49
+    hip_left = 50
+    hip_right = 51
+    spinal_cord = 52
+    gluteus_maximus_left = 53
+    gluteus_maximus_right = 54
+    gluteus_medius_left = 55
+    gluteus_medius_right = 56
+    gluteus_minimus_left = 57
+    gluteus_minimus_right = 58
+    autochthon_left = 59
+    autochthon_right = 60
+    iliopsoas_left = 61
+    iliopsoas_right = 62
+    sternum = 63
+    costal_cartilages = 64
+    subcutaneous_fat = 65
+    muscle = 66
+    inner_fat = 67
+    IVD = 68
+    vertebra_body = 69
+    vertebra_posterior_elements = 70
+    spinal_channel = 71
+    bone_other = 72
+
+
 class Full_Body_Instance(Abstract_lvl):
     skull = 1
     clavicula_right = 2