Compute metrics from segmentation

.gitignore

@@ -176,3 +176,7 @@ cython_debug/
 
 # Extra files
 /totalspineseg/models/nnUNet
+
+# More
+*.png
+*.csv

pyproject.toml

@@ -34,19 +34,15 @@ keywords = [
 ]
 dependencies = [
     "tqdm",
-    "numpy<2",
+    "numpy",
     "nibabel",
     "gryds",
     "torchio",
     "scipy",
     "pillow",
     "nilearn",
     "SimpleITK",
-    # We use nnunetv2==2.4.2 for nnUNetTrainer_DASegOrd0_NoMirroring
-    # https://github.com/MIC-DKFZ/nnUNet/issues/2480
-    # --verify_dataset_integrity not working in nnunetv2==2.4.2 do we need to update this when fixed
-    # https://github.com/MIC-DKFZ/nnUNet/issues/2144
-    "nnunetv2<=2.4.2",
+    "nnunetv2",
     "psutil",
 ]
 
@@ -76,6 +72,8 @@ totalspineseg_extract_levels = "totalspineseg.utils.extract_levels:main"
 totalspineseg_extract_alternate = "totalspineseg.utils.extract_alternate:main"
 totalspineseg_install_weights = "totalspineseg.utils.install_weights:main"
 totalspineseg_predict_nnunet = "totalspineseg.utils.predict_nnunet:main"
+totalspineseg_measure_seg = "totalspineseg.utils.measure_seg:main"
+totalspineseg_generate_reports = "totalspineseg.utils.generate_reports:main"
 
 [build-system]
 requires = ["pip>=23", "setuptools>=67"]

totalspineseg/resources/labels_maps/levels_maps.json

@@ -0,0 +1,27 @@
+{
+    "C1":1,
+    "C1-C2":2,
+    "C2-C3":3,
+    "C3-C4":4,
+    "C4-C5":5,
+    "C5-C6":6,
+    "C6-C7":7,
+    "C7-T1":8,
+    "T1-T2":9,
+    "T2-T3":10,
+    "T3-T4":11,
+    "T4-T5":12,
+    "T5-T6":13,
+    "T6-T7":14,
+    "T7-T8":15,
+    "T8-T9":16,
+    "T9-T10":17,
+    "T10-T11":18,
+    "T11-T12":19,
+    "T12-L1":20,
+    "L1-L2":21,
+    "L2-L3":22,
+    "L3-L4":23,
+    "L4-L5":24,
+    "L5-S":25
+}

totalspineseg/resources/labels_maps/tss_map.json

@@ -0,0 +1,54 @@
+{
+    "SC":1,
+    "CSF":2,
+    "C1":11,
+    "C2":12,
+    "C3":13,
+    "C4":14,
+    "C5":15,
+    "C6":16,
+    "C7":17,
+    "T1":21,
+    "T2":22,
+    "T3":23,
+    "T4":24,
+    "T5":25,
+    "T6":26,
+    "T7":27,
+    "T8":28,
+    "T9":29,
+    "T10":30,
+    "T11":31,
+    "T12":32,
+    "L1":41,
+    "L2":42,
+    "L3":43,
+    "L4":44,
+    "L5":45,
+    "L6":46,
+    "L7":47,
+    "sacrum":50,
+    "C2-C3":63,
+    "C3-C4":64,
+    "C4-C5":65,
+    "C5-C6":66,
+    "C6-C7":67,
+    "C7-T1":71,
+    "T1-T2":72,
+    "T2-T3":73,
+    "T3-T4":74,
+    "T4-T5":75,
+    "T5-T6":76,
+    "T6-T7":77,
+    "T7-T8":78,
+    "T8-T9":79,
+    "T9-T10":80,
+    "T10-T11":81,
+    "T11-T12":82,
+    "T12-L1":91,
+    "L1-L2":92,
+    "L2-L3":93,
+    "L3-L4":94,
+    "L4-L5":95,
+    "L5-S":100
+}