edits to evans index

totalsegmentator/bin/totalseg_evans_index.py

@@ -17,9 +17,9 @@
 from totalsegmentator.registration import calc_transform, apply_transform
 from totalsegmentator.python_api import totalsegmentator
 from totalsegmentator.nifti_ext_header import load_multilabel_nifti
-
 from totalsegmentator.serialization_utils import decompress_and_deserialize, filestream_to_nifti, serialize_and_compress, convert_to_serializable
 from totalsegmentator.dicom_io import dcm_to_nifti
+from totalsegmentator.config import send_usage_stats_application
 
 
 def run_models(ct_img):
@@ -97,8 +97,7 @@ def plot_slice_with_diameters(brain, start_b, end_b, start_v, end_v, evans_index
     return buf.getvalue()
 
 
-# def evans_index(brain_mask, ventricle_masks, skull_mask, ct_path, output_file, preview_file, models_parallel=False):
-def evans_index(ct_bytes, output_file, preview_file, f_type):
+def evans_index(ct_bytes, f_type):
     """
     ct_bytes: path to nifti file or 
               bytes object of zip file or
@@ -215,27 +214,20 @@ def evans_index(ct_bytes, output_file, preview_file, f_type):
 
 
 """
-# pip install antspyx
 cd ~/Downloads/evans_index/31103170_rot_large
-python ~/dev/TotalSegmentator/totalsegmentator/bin/totalseg_evans_index.py -b roi/brain.nii.gz -s roi/skull.nii.gz -v predicted/T552_ventricle_parts.nii.gz -c NR_01_SCHAEDEL/Sch_del_Syngo_1_0_Hr38_3_s003.nii -o evans_index_TEST.json -p evans_index_TEST.png
+python ~/dev/TotalSegmentator/totalsegmentator/bin/totalseg_evans_index.py -i ct_sm.nii.gz -o evans_index_TEST.json -p evans_index.png
 """
 if __name__ == "__main__":
     """
     For more documentation see resources/evans_index.md
     """
-    parser = argparse.ArgumentParser(description="Calc evans index.")
-    parser.add_argument("-b", "--brain_mask", type=lambda p: Path(p).resolve(), required=True,
-                        help="Path to brain mask file.")
-    parser.add_argument("-v", "--ventricle_masks", type=lambda p: Path(p).resolve(), required=True,
-                        help="Path to ventricle part masks.")
-    parser.add_argument("-s", "--skull_mask", type=lambda p: Path(p).resolve(), required=True,
-                        help="Path to skull masks.")
-    parser.add_argument("-c", "--ct_img", type=lambda p: Path(p).resolve(), required=True,
+    parser = argparse.ArgumentParser(description="Calculate evans index.")
+    parser.add_argument("-i", "--ct_img", type=lambda p: Path(p).resolve(), required=True,
                         help="Path to ct_img.")
     parser.add_argument("-o", "--output_file", type=lambda p: Path(p).resolve(), required=True,
                         help="json output file.")
     parser.add_argument("-p", "--preview_file", type=lambda p: Path(p).resolve(), required=True,
-                        help="Preview file of evans index to check if correct.")
+                        help="Preview PNG file of evans index to check if calculation is correct.")
     args = parser.parse_args()
 
     try:
@@ -265,3 +257,5 @@ def evans_index(ct_bytes, output_file, preview_file, f_type):
     # Save report png
     with open(args.preview_file, "wb") as f:
         f.write(final_result["report_png"])
+
+    send_usage_stats_application("evans_index")

totalsegmentator/bin/totalseg_get_modality.py

@@ -11,6 +11,7 @@
 import nibabel as nib
 import numpy as np
 
+from totalsegmentator.config import send_usage_stats_application
 
 """
 Additional requirements for this script:
@@ -84,6 +85,8 @@ def main():
     with open(args.output_file, "w") as f:
         f.write(json.dumps(res, indent=4))
 
+    send_usage_stats_application("get_modality")
+
 
 if __name__ == "__main__":
     main()

totalsegmentator/bin/totalseg_get_phase.py

@@ -12,7 +12,7 @@
 import numpy as np
 
 from totalsegmentator.python_api import totalsegmentator
-
+from totalsegmentator.config import send_usage_stats_application
 
 """
 Additional requirements for this script:
@@ -153,6 +153,8 @@ def main():
     with open(args.output_file, "w") as f:
         f.write(json.dumps(res, indent=4))
 
+    send_usage_stats_application("get_phase")
+
 
 if __name__ == "__main__":
     main()

totalsegmentator/config.py

@@ -171,6 +171,17 @@ def increase_prediction_counter():
         return config
 
 
+def get_config():
+    totalseg_dir = get_totalseg_dir()
+    totalseg_config_file = totalseg_dir / "config.json"
+    if totalseg_config_file.exists():
+        with open(totalseg_config_file) as f:
+            config = json.load(f)
+        return config
+    else:
+        return None
+
+
 def get_version():
     try:
         return pkg_resources.get_distribution("TotalSegmentator").version
@@ -238,3 +249,30 @@ def send_usage_stats(config, params):
         except Exception as e:
             # print(f"An Exception occurred: {e}")
             pass
+
+
+def send_usage_stats_application(application_name):
+    config = get_config()
+    if config is not None and config["send_usage_stats"]:
+
+        try:
+            st = time.time()
+            url = "http://backend.totalsegmentator.com:80/"
+            r = requests.post(url + "log_totalseg_application_run",
+                              json={"totalseg_id": config["totalseg_id"],
+                                    "application": application_name,
+                                    "platform": platform.system(),
+                                    "machine": platform.machine(),
+                                    "version": get_version(),
+                                    "python_version": sys.version,
+                                    "cuda_available": torch.cuda.is_available()
+                                    }, timeout=5)
+            # if r.ok:
+            #     print(f"status: {r.json()['status']}")
+            # else:
+            #     print(f"status code: {r.status_code}")
+            #     print(f"message: {r.json()['message']}")
+            # print(f"Request took {time.time()-st:.3f}s")
+        except Exception as e:
+            # print(f"An Exception occurred: {e}")
+            pass