seqseg 2.1.8__tar.gz → 2.2.0__tar.gz

{seqseg-2.1.8 → seqseg-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seqseg
-Version: 2.1.8
+Version: 2.2.0
 Summary: A deep learning-based medical image blood vessel tracking and segmentation tool.
 Author-email: Numi Sveinsson Cepero <numi@berkeley.com>
 License: Apache-2.0

{seqseg-2.1.8 → seqseg-2.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "seqseg"
-version = "2.1.8"
+version = "2.2.0"
 description = "A deep learning-based medical image blood vessel tracking and segmentation tool."
 readme = "README.md"
 requires-python = ">=3.9"
@@ -54,7 +54,7 @@ homepage = "https://github.com/numisveinsson/SeqSeg"
 repository = "https://github.com/numisveinsson/SeqSeg"
 
 [tool.setuptools]
-package-data = { "seqseg" = ["config/*.yaml"] }
+package-data = { "seqseg" = ["config/*.yaml", "config/sampler/*.yaml", "config/sampler/*.yml"] }
 
 [project.optional-dependencies]
 dev = [

{seqseg-2.1.8 → seqseg-2.2.0}/seqseg/__init__.py

@@ -12,6 +12,7 @@ __all__ = (
     "load_yaml_config",
     "run_classic_batch",
     "run_plus_batch",
+    "run_global_prediction",
     "bootstrap_simvascular_project",
     "bootstrap_simvascular_project_batch",
     "run_global_centerline_single",
@@ -21,6 +22,7 @@ __all__ = (
     "seeds_to_potential_branches",
     "TracingOptions",
     "run_tracing",
+    "continue_tracing",
 )
 
 
@@ -69,6 +71,10 @@ def __getattr__(name: str):
         from seqseg.pipeline.plus import run_plus_batch
 
         return run_plus_batch
+    if name == "run_global_prediction":
+        from seqseg.pipeline.predict import run_global_prediction
+
+        return run_global_prediction
     if name == "bootstrap_simvascular_project":
         from seqseg.pipeline.post import bootstrap_simvascular_project
 
@@ -105,4 +111,8 @@ def __getattr__(name: str):
         from seqseg.api import run_tracing
 
         return run_tracing
+    if name == "continue_tracing":
+        from seqseg.api import continue_tracing
+
+        return continue_tracing
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

{seqseg-2.1.8 → seqseg-2.2.0}/seqseg/api.py

@@ -107,6 +107,7 @@ def seeds_to_potential_branches(
             raise ValueError("old_point and new_point must have length 3")
         step = create_step_dict(old, r, new, r, None)
         step["connection"] = [0, 0]
+        step["init_seed"] = True
         out.append(step)
     return out
 
@@ -203,3 +204,36 @@ def run_tracing(
         force_cpu=opts.force_cpu,
     )
     return trace_centerline_from_context(ctx)
+
+
+def continue_tracing(
+    case_dir: str,
+    extra_steps: int,
+    seeds: Optional[Sequence[Union[BranchSeed, Mapping[str, Any], Sequence[Any]]]] = None,
+    *,
+    max_n_branches: Optional[int] = None,
+    max_n_steps_per_branch: Optional[int] = None,
+    force_cpu: Optional[bool] = None,
+) -> TracingResult:
+    """
+    Continue a CLI/batch run from ``{case_dir}/checkpoint`` for ``extra_steps`` steps.
+
+    ``seeds`` accept the same forms as :func:`seeds_to_potential_branches`;
+    they are traced as new initialization seeds once the open branch ends.
+    Outputs are rewritten with the new step count and the checkpoint is
+    replaced, so the run can be continued again.
+    """
+    from seqseg.pipeline.continue_run import run_continue
+
+    triples = [
+        [s["old point"], s["point"], s["radius"]]
+        for s in seeds_to_potential_branches(seeds or [])
+    ]
+    return run_continue(
+        case_dir,
+        extra_steps,
+        seeds=triples,
+        max_n_branches=max_n_branches,
+        max_n_steps_per_branch=max_n_steps_per_branch,
+        force_cpu=force_cpu,
+    )

{seqseg-2.1.8 → seqseg-2.2.0}/seqseg/cli.py

@@ -16,11 +16,19 @@ import faulthandler
 import numpy as np
 
 from seqseg.citations import print_citation_banner
-from seqseg.config_models import AlgorithmConfig, NnUNetModelSpec, load_yaml_config
+from seqseg.config_models import (
+    AlgorithmConfig,
+    NnUNetModelSpec,
+    load_yaml_config,
+    resolve_nnunet_model_folder,
+)
 from seqseg.modules import sitk_functions as sf
 from seqseg.modules.datasets import get_testing_samples
+from seqseg.modules.checkpoint import has_checkpoint
 from seqseg.pipeline.classic import run_classic_batch
+from seqseg.pipeline.continue_run import run_continue, seeds_from_json, seeds_from_xyzr
 from seqseg.pipeline.plus import run_plus_batch
+from seqseg.pipeline.predict import run_global_prediction
 from seqseg.pipeline.single_trace import prepare_single_image_dataset
 from seqseg.pipeline.post import (
     bootstrap_simvascular_project,
@@ -190,6 +198,20 @@ def _add_plus_trace_args(p: argparse.ArgumentParser) -> None:
         type=str,
         default="Dataset012_COROASOCACT",
     )
+    p.add_argument(
+        "-global_seg_dir",
+        "--global_seg_dir",
+        "--global-seg-dir",
+        dest="global_seg_dir",
+        default=None,
+        type=str,
+        help=(
+            "Folder of per-case global segmentations. Skips the global "
+            "nnU-Net prediction and does not use global weights. "
+            "Accepts {case}_segmentation.mha with optional "
+            "{case}_probability.mha, or {case}{img_ext}"
+        ),
+    )
 
 
 def _seqseg_version() -> str:
@@ -244,6 +266,15 @@ def _validate_trace_batch(ns: argparse.Namespace) -> None:
         ns.start_seg = start_seg
 
 
+def _resolve_run_weights(spec: NnUNetModelSpec) -> str:
+    """Pick the trainer folder, or exit when the dataset has several."""
+    try:
+        return resolve_nnunet_model_folder(spec)
+    except ValueError as e:
+        print(f"seqseg: {e}", file=sys.stderr)
+        sys.exit(2)
+
+
 def _cmd_trace_batch(ns: argparse.Namespace) -> None:
     _validate_trace_batch(ns)
     faulthandler.enable()
@@ -265,7 +296,8 @@ def _cmd_trace_batch(ns: argparse.Namespace) -> None:
         fold=ns.fold,
         scale=ns.scale,
     )
-    dir_model_weights = spec.model_folder()
+    dir_model_weights = _resolve_run_weights(spec)
+    print(f"Using nnU-Net weights from:\n  {dir_model_weights}")
 
     testing_samples, directory_data = get_testing_samples(ns.train_dataset, data_dir)
     print("Testing samples about to run:")
@@ -308,6 +340,7 @@ def _cmd_trace_batch(ns: argparse.Namespace) -> None:
         simvascular=bool(ns.simvascular),
         force_cpu=bool(ns.force_cpu),
         start_seg_path=ns.start_seg,
+        config_name=ns.config_name,
         start_time_global=t0,
     )
     print("\nTotal calculation time for all cases is: ")
@@ -328,24 +361,44 @@ def _cmd_trace_plus_batch(ns: argparse.Namespace) -> None:
     except Exception as e:  # noqa: BLE001
         print(e)
 
-    dir_model_weights_seqseg = NnUNetModelSpec(
-        train_dataset=ns.seqseg_train_dataset,
-        nnunet_type=ns.seqseg_test_name,
-        results_path=ns.nnunet_results_path,
-        fold=ns.seqseg_fold,
-        scale=ns.seqseg_scale,
-    ).model_folder()
-    dir_model_weights_global = NnUNetModelSpec(
-        train_dataset=ns.global_train_dataset,
-        nnunet_type=ns.global_test_name,
-        results_path=ns.nnunet_results_path,
-        fold=ns.global_fold,
-        scale=ns.global_scale,
-    ).model_folder()
+    dir_model_weights_seqseg = _resolve_run_weights(
+        NnUNetModelSpec(
+            train_dataset=ns.seqseg_train_dataset,
+            nnunet_type=ns.seqseg_test_name,
+            results_path=ns.nnunet_results_path,
+            fold=ns.seqseg_fold,
+            scale=ns.seqseg_scale,
+        )
+    )
+    global_seg_dir = getattr(ns, "global_seg_dir", None)
+    if global_seg_dir:
+        global_seg_dir = os.path.abspath(os.path.expanduser(global_seg_dir))
+        if not os.path.isdir(global_seg_dir):
+            print(
+                "seqseg run plus batch: global segmentation directory not found: "
+                f"{global_seg_dir}",
+                file=sys.stderr,
+            )
+            sys.exit(2)
+        dir_model_weights_global = None
+    else:
+        dir_model_weights_global = _resolve_run_weights(
+            NnUNetModelSpec(
+                train_dataset=ns.global_train_dataset,
+                nnunet_type=ns.global_test_name,
+                results_path=ns.nnunet_results_path,
+                fold=ns.global_fold,
+                scale=ns.global_scale,
+            )
+        )
     print("Using nnUNet model weights from:")
     print(dir_model_weights_seqseg)
-    print("Using nnUNet model weights for global segmentation from:")
-    print(dir_model_weights_global)
+    if global_seg_dir:
+        print("Using global segmentations from:")
+        print(global_seg_dir)
+    else:
+        print("Using nnUNet model weights for global segmentation from:")
+        print(dir_model_weights_global)
 
     testing_samples, directory_data = get_testing_samples(ns.seqseg_train_dataset, data_dir)
     print("Testing samples about to run:")
@@ -387,6 +440,8 @@ def _cmd_trace_plus_batch(ns: argparse.Namespace) -> None:
         simvascular=bool(ns.simvascular),
         force_cpu=bool(ns.force_cpu),
         start_seg_path=ns.start_seg,
+        global_seg_dir=global_seg_dir,
+        config_name=ns.config_name,
         start_time_global=t0,
     )
     print("\nTotal calculation time is: ")
@@ -529,12 +584,104 @@ def _cmd_trace_single(ns: argparse.Namespace) -> None:
         simvascular=bool(ns.simvascular),
         force_cpu=bool(ns.force_cpu),
         start_seg_path=getattr(ns, "start_seg", None),
+        config_name=ns.config_name,
         start_time_global=t0,
     )
     print("\nTotal calculation time for run single: ")
     print(f"{((time.time() - t0) / 60):.2f} min\n")
 
 
+def _cmd_trace_continue(ns: argparse.Namespace) -> None:
+    faulthandler.enable()
+    t0 = time.time()
+    case_dir = os.path.abspath(os.path.expanduser(ns.case_dir))
+    if not has_checkpoint(case_dir):
+        print(
+            f"seqseg run continue: no checkpoint in {case_dir}/checkpoint. "
+            "Only runs made with a SeqSeg version that writes checkpoints "
+            "can be continued.",
+            file=sys.stderr,
+        )
+        sys.exit(2)
+    if ns.extra_steps < 0:
+        print("seqseg run continue: --extra-steps must be >= 0", file=sys.stderr)
+        sys.exit(2)
+
+    seeds: List[list] = []
+    try:
+        if ns.seeds_json:
+            if not os.path.isfile(ns.seeds_json):
+                print(f"--seeds-json not found: {ns.seeds_json}", file=sys.stderr)
+                sys.exit(2)
+            with open(os.path.join(case_dir, "checkpoint", "manifest.json"),
+                      encoding="utf-8") as f:
+                case = json.load(f).get("case")
+            seeds += seeds_from_json(ns.seeds_json, case)
+        if ns.seed:
+            seeds += seeds_from_xyzr(
+                [list(map(float, s)) for s in ns.seed],
+                tangent=tuple(ns.tangent),
+                seed_step=ns.seed_step,
+            )
+    except ValueError as e:
+        print(f"seqseg run continue: {e}", file=sys.stderr)
+        sys.exit(2)
+
+    run_continue(
+        case_dir,
+        ns.extra_steps,
+        seeds=seeds,
+        max_n_branches=ns.max_n_branches,
+        max_n_steps_per_branch=ns.max_n_steps_per_branch,
+        force_cpu=True if ns.force_cpu else None,
+    )
+    print("\nTotal calculation time for run continue: ")
+    print(f"{((time.time() - t0) / 60):.2f} min\n")
+
+
+def _cmd_run_global(ns: argparse.Namespace) -> None:
+    model_folder = os.path.abspath(os.path.expanduser(ns.model_folder))
+    if not os.path.isdir(model_folder):
+        print(
+            f"seqseg run global: model folder not found: {model_folder}",
+            file=sys.stderr,
+        )
+        sys.exit(2)
+    outdir = os.path.abspath(os.path.expanduser(ns.outdir))
+    image = None
+    image_dir = None
+    if ns.image:
+        image = os.path.abspath(os.path.expanduser(ns.image))
+        if not os.path.isfile(image):
+            print(
+                f"seqseg run global: image not found: {image}",
+                file=sys.stderr,
+            )
+            sys.exit(2)
+    else:
+        image_dir = os.path.abspath(os.path.expanduser(ns.image_dir))
+        if not os.path.isdir(image_dir):
+            print(
+                f"seqseg run global: image folder not found: {image_dir}",
+                file=sys.stderr,
+            )
+            sys.exit(2)
+    try:
+        run_global_prediction(
+            model_folder=model_folder,
+            outdir=outdir,
+            image=image,
+            image_dir=image_dir,
+            img_ext=ns.img_ext,
+            fold=ns.fold,
+            scale=ns.scale,
+            force_cpu=bool(ns.force_cpu),
+        )
+    except FileNotFoundError as e:
+        print(f"seqseg run global: {e}", file=sys.stderr)
+        sys.exit(2)
+
+
 def _cmd_doctor(ns: argparse.Namespace) -> None:
     import importlib
 
@@ -709,8 +856,9 @@ def _cmd_train_prepare(ns: argparse.Namespace) -> None:
         )
     elif result.removed_staging:
         print(
-            "  Extracted volumes were linked into nnU-Net raw and the "
-            "temporary folder was removed."
+            "  Extracted subvolumes were removed after conversion. "
+            "done.txt and the .txt/.csv metadata were kept in\n"
+            f"  {result.extracted_dir}"
         )
     else:
         kind = "Whole volumes" if ns.global_volumes else "Patches"
@@ -829,7 +977,7 @@ def _build_parser() -> argparse.ArgumentParser:
 
     run_grp = sub.add_parser(
         "run",
-        help="Run segmentation and vessel tracing (batch, plus, or single volume)",
+        help="Run segmentation and vessel tracing (batch, plus, single, or global)",
     )
     run_sub = run_grp.add_subparsers(dest="run_cmd", required=True)
 
@@ -944,6 +1092,109 @@ def _build_parser() -> argparse.ArgumentParser:
     )
     p_single.set_defaults(_handler=_cmd_trace_single)
 
+    p_continue = run_sub.add_parser(
+        "continue",
+        help="Continue a traced case from its checkpoint for more steps",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    p_continue.add_argument(
+        "--case-dir",
+        required=True,
+        type=str,
+        help="Case output folder holding checkpoint/ (e.g. <outdir>/3d_fullres_case001)",
+    )
+    p_continue.add_argument(
+        "--extra-steps",
+        required=True,
+        type=int,
+        help="Steps to add on top of the steps already taken",
+    )
+    p_continue.add_argument(
+        "--seed",
+        action="append",
+        nargs=4,
+        type=float,
+        metavar=("X", "Y", "Z", "R"),
+        help="New seed traced after the open branch ends (repeat for multiple)",
+    )
+    p_continue.add_argument(
+        "--tangent",
+        nargs=3,
+        type=float,
+        default=[0.0, 0.0, 1.0],
+        metavar=("TX", "TY", "TZ"),
+        help="Used with --seed to place the paired old point",
+    )
+    p_continue.add_argument(
+        "--seed-step",
+        default=1.0,
+        type=float,
+        help="Physical step along --tangent for old-point when using --seed",
+    )
+    p_continue.add_argument(
+        "--seeds-json",
+        default=None,
+        type=str,
+        help="New seeds as [old_point, new_point, radius] triples: a seeds.json "
+        "(entry matching the case), one case object, or a bare list",
+    )
+    p_continue.add_argument(
+        "--max-n-branches",
+        default=None,
+        type=int,
+        help="Raise the branch cap (default: value from the checkpoint)",
+    )
+    p_continue.add_argument(
+        "--max-n-steps-per-branch",
+        default=None,
+        type=int,
+        help="Change the per-branch cap (default: value from the checkpoint)",
+    )
+    p_continue.add_argument(
+        "-cpu",
+        "--cpu",
+        dest="force_cpu",
+        action="store_true",
+        help="Force nnU-Net inference on CPU even if a GPU is available",
+    )
+    p_continue.set_defaults(_handler=_cmd_trace_continue)
+
+    p_global = run_sub.add_parser(
+        "global",
+        help="Whole-volume nnU-Net prediction (one image or a folder)",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    global_src = p_global.add_mutually_exclusive_group(required=True)
+    global_src.add_argument("--image", type=str, help="Input volume path")
+    global_src.add_argument(
+        "--image-dir",
+        type=str,
+        help="Folder of input volumes (not a SeqSeg dataset)",
+    )
+    p_global.add_argument("--outdir", required=True, type=str)
+    p_global.add_argument(
+        "--model-folder",
+        required=True,
+        type=str,
+        help="nnU-Net trainer folder (…/nnUNetTrainer__nnUNetPlans__3d_fullres)",
+    )
+    p_global.add_argument("--fold", default="all", type=str)
+    p_global.add_argument("--scale", default=1.0, type=float)
+    p_global.add_argument(
+        "--img-ext",
+        default=None,
+        type=str,
+        help="Volume extension when using --image-dir (for example .nii.gz)",
+    )
+    p_global.add_argument(
+        "-cpu",
+        "--cpu",
+        dest="force_cpu",
+        action="store_true",
+        help="Force nnU-Net inference on CPU even if a GPU is available",
+    )
+    p_global.set_defaults(_handler=_cmd_run_global)
+
     post = sub.add_parser("post", help="Post-process existing outputs")
     post_sub = post.add_subparsers(dest="post_cmd", required=True)
     gcl = post_sub.add_parser("global-centerline")
@@ -1061,8 +1312,9 @@ def _build_parser() -> argparse.ArgumentParser:
         default=None,
         type=str,
         help="Optional scratch directory for extracted patches or whole volumes. "
-        "Default: <parent of nnUNet_raw>/_seqseg_extracted, removed after "
-        "conversion. Pass this to keep extracts or resume with --skip-sample.",
+        "Default: nnUNet_raw/DatasetXXX_*/_seqseg_extracted. Subvolumes are "
+        "removed after conversion; done.txt and .txt/.csv metadata are kept. "
+        "Pass this to keep a copy elsewhere.",
     )
     p_prep.add_argument(
         "--name",
@@ -1094,7 +1346,7 @@ def _build_parser() -> argparse.ArgumentParser:
         "-config_name",
         default="default_mm",
         type=str,
-        help="Sampler YAML name/path (from vascular-segment-sampler)",
+        help="Sampler YAML name/path (default_mm, default_cm, test, or a file)",
     )
     p_prep.add_argument(
         "--nnunet-raw",
@@ -1156,7 +1408,8 @@ def _build_parser() -> argparse.ArgumentParser:
     p_prep.add_argument(
         "--keep-extracted",
         action="store_true",
-        help="Keep <nnunet-root>/_seqseg_extracted after conversion into nnUNet_raw",
+        help="Keep extracted subvolumes in nnUNet_raw/DatasetXXX_*/_seqseg_extracted "
+        "after conversion into nnUNet_raw",
     )
     p_prep.add_argument(
         "--configuration",
@@ -1179,8 +1432,9 @@ def _build_parser() -> argparse.ArgumentParser:
     p_prep.add_argument(
         "--preprocess-only",
         action="store_true",
-        help="Preprocess another configuration from an existing raw dataset "
-        "and plans file. Does not extract or convert subvolumes",
+        help="Use an existing nnUNet_raw dataset. Plans and preprocesses it "
+        "when plans are missing; otherwise resamples --configuration. "
+        "Does not extract or convert subvolumes",
     )
     p_prep.set_defaults(_handler=_cmd_train_prepare, img_ext=None)
 
@@ -1220,7 +1474,13 @@ def _build_parser() -> argparse.ArgumentParser:
         action="store_true",
         help="Continue training from checkpoint_latest.pth (nnU-Net --c)",
     )
-    p_nn.add_argument("--trainer", default="nnUNetTrainer", type=str)
+    p_nn.add_argument(
+        "--trainer",
+        default=None,
+        type=str,
+        help="nnU-Net trainer class. Default: nnUNetTrainer, or "
+        "nnUNetTrainerNoDeepSupervision when the plan downsamples at most once",
+    )
     p_nn.add_argument("--plans", default="nnUNetPlans", type=str)
     p_nn.add_argument(
         "--cleanup",

seqseg-2.2.0/seqseg/config/global_coro_retrace.yaml

@@ -0,0 +1,59 @@
+# Coronary config with retracing prevention on.
+# Same settings as global_coro.yaml except PREVENT_RETRACE.
+# if we are tracing a segmentation or predicting a segmentation as we go
+# True if we have a segmentation, False if we are predicting
+SEGMENTATION: False # usually False
+
+DEBUG: False
+DEBUG_STEP: 100
+
+ANIMATION: True # to write out animation files
+ANIMATION_STEPS: 3 # write out animation every x steps
+
+RETRACE: False # retrace strategry
+TIME_ANALYSIS: False # if we want to write out how long each step take
+TREE_ANALYSIS: False
+
+VOLUME_SIZE_RATIO: 5.5 # default 5, 5.5 for coronaries, 4 for segs
+MAGN_RADIUS: 1
+ADD_RADIUS: 0.3
+MAX_PERC_ENLARGE: 0.33 # if percent of blood in a given volume goes above this, we try enlarging volume, default 0.33 for coronaries
+MIN_RADIUS: 0.3 # mm (keep in mm)
+MIN_RES: 5
+CENTERLINE_EXTRACTION_VMTK: False # if we want to extract centerline using VMTK
+CENTERLINE_MERGE_METHOD: clean # clean (vtkCleanPolyData) or tree
+TYPE_CENT: profileidlist #profileidlist # can also be profileidlist / pointlist
+
+NR_CHANCES: 3
+NR_ALLOW_RETRACE_STEPS: 10
+PREVENT_RETRACE: True
+SORT_NEXT: True
+MERGE_NEXT: False
+
+ASSEMBLY_EVERY_N: 20 # add to assembly every N steps
+USE_BUFFER: True # buffer the assembly (so not to mess with retrace prevention)
+BUFFER_N: 20 # add to assembly steps buff_N steps ago
+WEIGHTED_ASSEMBLY: True # if assembly should be weighted
+WEIGHT_TYPE: gaussian # type of weighting for assembly
+CENT_MAX_SPACING: 0.3 # mm; max spacing per dim for final assembly (refine only)
+
+FORCEFUL_SIDEBRANCH: False
+FORCEFUL_SIDEBRANCH_MAGN_RADIUS: 1.1
+
+MEGA_SUBVOLUME: False # extract centerline from previous N steps, instead of just 1
+NR_MEGA_SUB: 3 # how many steps to assemble into mega subvolume
+
+STOP_PRE: True # whether to stop tracing prematurely, if True then options below will be used
+STOP_RADIUS: 0.4 # (mm) 0.48 if radius goes below, stop tracing
+MAX_STEPS_BRANCH: 100 # max num of steps per branch, stop when reached
+
+RESTART_BRANCH: True
+
+# SimVascular: after each completed branch, write one .ctgr contour group (2D
+# contours along that branch's .pth) using the live global probability assembly.
+SIMVASCULAR_CONTOURS: True
+SIMVASCULAR_CONTOUR_ISO: 0.5
+SIMVASCULAR_CONTOUR_STRIDE: 2
+SIMVASCULAR_CONTOUR_HALF_EXTENT_MM: 50.0
+# closest_to_path | largest — see simvascular_contour.py
+SIMVASCULAR_CONTOUR_COMPONENT: closest_to_path

seqseg-2.2.0/seqseg/config/sampler/default_cm.yaml

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+# SeqSeg sampler config for centimeter data (VMR / SimVascular). Overlay on default_mm.yaml.
+# Adapted from vascular-segment-sampler 0.7.0 config/default_cm.yaml.
+# Image, truth, surface, and centerline must all be in cm.
+
+RADIUS_ADD: 0.02 # absolute add to radius in cm (0.2 mm)
+LARGE_RADIUS_THRESH: 0.4 # radius in cm at which MOVE_SLOWER_LARGE applies (4 mm)

seqseg-2.2.0/seqseg/config/sampler/default_mm.yaml

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+# SeqSeg sampler default for millimeter data. Base for every named sampler config.
+# Adapted from vascular-segment-sampler 0.7.0 config/default_mm.yaml, keeping only
+# the keys the sampler requires for `seqseg train prepare`.
+# Image, truth, surface, and centerline must all be in mm.
+# For centimeter data (VMR), use --config-name default_cm.
+#
+# The optional outputs below are off. Turning one on in your own YAML also needs
+# its companion keys, e.g. RESAMPLE_SIZE with RESAMPLE_VOLUMES, OUTLET_CLASSES
+# with WRITE_SURFACE/WRITE_CENTERLINE, N_SLICES and RESAMPLE_CROSS_IMG with
+# WRITE_TRAJECTORIES/WRITE_CROSS_SECTIONAL.
+
+DATASET_NAME: 'other'
+
+EXTRACT_VOLUMES: True
+WRITE_SAMPLES: True
+WRITE_IMG: True
+BINARIZE: True
+REMOVE_OTHER: True # Remove other unconnected vessels in gt volume, can cause problems where vessels are close
+ROTATE_VOLUMES: False
+RESAMPLE_VOLUMES: False
+CAPFREE: False # whether to require a certain amount of cap-free volume
+CAPFREE_PROP: 0.0 # how much of volume must be cap free, per sidelength
+
+WRITE_SURFACE: False
+WRITE_CENTERLINE: False
+WRITE_VTK: False
+WRITE_DISCRETE_CENTERLINE: False
+WRITE_OUTLET_STATS: False
+WRITE_CROSS_SECTIONAL: False
+WRITE_TRAJECTORIES: False
+
+# MOVE_DIST, MU_SIZE, SIGMA_SHIFT are multiples of local radius. RADIUS_ADD and
+# LARGE_RADIUS_THRESH are absolute, in the centerline's unit.
+MOVE_DIST: 1.5 # how far to move along centerline between sampling, in radii
+MOVE_SLOWER_LARGE: 0.5 # how much slower for bigger vessels
+MOVE_SLOWER_BIFURC: 0.5 # how much slower at bifurcations
+LARGE_RADIUS_THRESH: 4.0 # radius in mm at which MOVE_SLOWER_LARGE applies
+RADIUS_ADD: 0.2 # absolute add to radius in mm (before RADIUS_SCALE)
+RADIUS_SCALE: 1 # keep 1 when image and centerline units match
+MU_SIZE: 5 # mean for subvolume-radius ratio
+SIGMA_SIZE: 0.8 # standard deviation for subvolume-radius ratio
+MU_SHIFT: 0 # mean for subvolume shift off centerline
+SIGMA_SHIFT: 0.8 # standard deviation for subvolume shift off centerline
+NUMBER_SAMPLES: 3 # samples at each point along vessel
+NUMBER_SAMPLES_BIFURC: 5 # samples at a bifurcation
+NUMBER_SAMPLES_START: 3 # samples at start of vessel (first 5%)

seqseg-2.2.0/seqseg/config/sampler/test.yml

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+# SeqSeg smoke-test sampler overlay on default_mm.yaml.
+# Adapted from vascular-segment-sampler 0.7.0 config/test.yml.
+# One extract per point, long steps, and a hard cap so a case finishes quickly.
+
+MAX_SAMPLES: 12
+
+MOVE_DIST: 8 # centerline step, in radii (default 1.5)
+MOVE_SLOWER_LARGE: 1
+MOVE_SLOWER_BIFURC: 1
+
+NUMBER_SAMPLES: 1
+NUMBER_SAMPLES_BIFURC: 1
+NUMBER_SAMPLES_START: 1