Modify nesvor running script.

fetal_brain_utils/cli/run_nesvor_docker.py

@@ -19,7 +19,7 @@
 DATA_PATH = Path("/media/tsanchez/tsanchez_data/data/data")
 AUTO_MASK_PATH = "/media/tsanchez/tsanchez_data/data/out_anon/masks"
 
-BATCH_SIZE = 8192
+BATCH_SIZE = 4096
 NESVOR_VERSION = "v0.5.0"
 
 
@@ -34,15 +34,21 @@ def iterate_subject(
     target_res,
     config,
     nesvor_version,
+    batch_size,
+    recon_type,
     mask_input,
     fake_run,
+    extra_commands,
 ):
     if participant_label:
         if sub not in participant_label:
             return
     if sub not in bids_layout.get_subjects():
         print(f"Subject {sub} not found in {data_path}")
         return
+
+    if recon_type == "svr":
+        assert len(target_res) == 1, "Only one resolution can be used for SVR."
     # if sub not in sub_ses_dict:
     #    print(f"Subject {sub} not found in {data_path}")
     #    return
@@ -122,33 +128,38 @@ def iterate_subject(
                 output_file = str(out / out_base) + "_misaligned.nii.gz"
             output_json = str(output_sub_ses / out_base) + ".json"
             if i == 0:
+                nesvor_arg = "svr" if recon_type == "svr" else "reconstruct"
                 cmd = (
                     f"docker run --gpus '\"device=0\"' "
                     f"-v {mount_base}:/data "
                     f"-v {output_sub_ses}:/out "
-                    # f"-v /home/tsanchez/Documents/mial/repositories/NeSVoR/nesvor:/usr/local/NeSVoR/nesvor "
-                    f"junshenxu/nesvor:{nesvor_version} nesvor reconstruct "
+                    f"junshenxu/nesvor:{nesvor_version} nesvor {nesvor_arg} "
                     f"--input-stacks {img_str} "
                     f"--stack-masks {mask_str} "
                     f"--output-volume {output_file} "
-                    f"--output-resolution {res} "
-                    f"--output-model {model} "
-                    f"--n-levels-bias 1 "
-                    f"--batch-size {BATCH_SIZE} "
-                    " --n-proc-n4 1 "
                 )
+                if recon_type == "nesvor":
+                    cmd += (
+                        f"--output-resolution {res} "
+                        f"--output-model {model} "
+                        f"--n-levels-bias 1 "
+                        f"--batch-size {batch_size} "
+                        " --n-proc-n4 1 "
+                    )
                 if nesvor_version == "v0.5.0":
                     cmd += "--bias-field-correction"
+                if extra_commands != "":
+                    cmd += f" {extra_commands}"
             else:
                 cmd = (
                     f"docker run --gpus '\"device=0\"' "
                     f"-v {output_sub_ses}:/out "
-                    f"junshenxu/nesvor:v0.1.0 nesvor sample-volume "
+                    f"junshenxu/nesvor:{nesvor_version} nesvor sample-volume "
                     f"--input-model {model} "
                     f"--output-resolution {res} "
                     f"--output-volume {output_file} "
                     f"--output-resolution {res} "
-                    f"--inference-batch-size 16384"
+                    f"--inference-batch-size {batch_size*2}"
                 )
             conf["info"] = {
                 "reconstruction": "NeSVoR",
@@ -204,6 +215,28 @@ def main(argv=None):
         default=True,
         help="Whether the input stacks should be masked prior to computation.",
     )
+
+    p.add_argument(
+        "--batch_size",
+        type=int,
+        default=BATCH_SIZE,
+        help="Batch size for the NeSVoR pipeline.",
+    )
+
+    p.add_argument(
+        "--recon_type",
+        type=str,
+        default="nesvor",
+        choices=["nesvor", "svr"],
+        help="Types of reconstruction to be run: train a NeSVoR model or just run SVR.",
+    )
+
+    p.add_argument(
+        "--extra_commands",
+        type=str,
+        default="",
+        help="Extra commands to be added to the NeSVoR command.",
+    )
     args = p.parse_args(argv)
 
     data_path = Path(args.data_path).resolve()
@@ -219,15 +252,17 @@ def main(argv=None):
     iterate = partial(
         iterate_subject,
         bids_layout=bids_layout,
-        # sub_ses_dict=sub_ses_dict,
         data_path=data_path,
         output_path=out_path,
         mask_base_path=masks_folder,
         participant_label=args.participant_label,
         target_res=args.target_res,
         config=config,
         nesvor_version=args.version,
+        batch_size=args.batch_size,
         mask_input=args.mask_input,
+        recon_type=args.recon_type,
+        extra_commands=args.extra_commands,
         fake_run=args.fake_run,
     )
     for sub, config_sub in params.items():