simcortexpp 0.1.0__py3-none-any.whl

simcortexpp/cli/main.py

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+from __future__ import annotations
+
+import sys
+import subprocess
+import typer
+from typing import List
+
+from simcortexpp.preproc.fs_to_mni import app as fs_to_mni_app
+from simcortexpp.initsurf.generate import main as initsurf_generate
+
+
+app = typer.Typer(help="SimCortexPP (SCPP) CLI")
+
+def run_module(module: str, overrides: List[str], torchrun: bool = False, nproc: int = 1) -> int:
+    if torchrun:
+        cmd = ["torchrun", f"--nproc_per_node={nproc}", "-m", module]
+    else:
+        cmd = [sys.executable, "-m", module]
+    cmd += (overrides or [])
+    return subprocess.call(cmd)
+
+# Preprocessing
+app.add_typer(fs_to_mni_app, name="fs-to-mni", help="FreeSurfer -> MNI preprocessing")
+
+# Segmentation group
+seg_app = typer.Typer(help="Segmentation (3D U-Net) stage")
+app.add_typer(seg_app, name="seg")
+
+initsurf_app = typer.Typer(help="Initial surface generation (from seg predictions)")
+
+@seg_app.command("train")
+def seg_train(
+    overrides: List[str] = typer.Argument(None, help="Hydra overrides"),
+    torchrun: bool = typer.Option(False, "--torchrun", help="Launch training with torchrun for DDP"),
+    nproc_per_node: int = typer.Option(1, "--nproc-per-node", help="GPUs per node for torchrun"),
+):
+    code = run_module("simcortexpp.seg.train", overrides or [], torchrun=torchrun, nproc=nproc_per_node)
+    raise typer.Exit(code)
+
+@seg_app.command("infer")
+def seg_infer(overrides: List[str] = typer.Argument(None, help="Hydra overrides")):
+    code = run_module("simcortexpp.seg.inference", overrides or [])
+    raise typer.Exit(code)
+
+@seg_app.command("eval")
+def seg_eval(overrides: List[str] = typer.Argument(None, help="Hydra overrides")):
+    code = run_module("simcortexpp.seg.eval", overrides or [])
+    raise typer.Exit(code)
+
+@initsurf_app.command("generate")
+def initsurf_generate_cmd(overrides: List[str] = typer.Argument(None, help="Hydra overrides")):
+    code = run_module("simcortexpp.initsurf.generate", overrides or [])
+    raise typer.Exit(code)
+
+app.add_typer(initsurf_app, name="initsurf")
+
+# --- add near seg_app / initsurf_app ---
+deform_app = typer.Typer(help="Stage 4 — Deformation: train / infer / eval")
+app.add_typer(deform_app, name="deform")
+
+@deform_app.command("train")
+def deform_train(
+    overrides: List[str] = typer.Argument(None, help="Hydra overrides"),
+    torchrun: bool = typer.Option(False, "--torchrun", help="Launch training with torchrun for DDP"),
+    nproc_per_node: int = typer.Option(1, "--nproc-per-node", help="GPUs per node for torchrun"),
+):
+    code = run_module("simcortexpp.deform.train", overrides or [], torchrun=torchrun, nproc=nproc_per_node)
+    raise typer.Exit(code)
+
+@deform_app.command("infer")
+def deform_infer(overrides: List[str] = typer.Argument(None, help="Hydra overrides")):
+    code = run_module("simcortexpp.deform.inference", overrides or [])
+    raise typer.Exit(code)
+
+@deform_app.command("eval")
+def deform_eval(overrides: List[str] = typer.Argument(None, help="Hydra overrides")):
+    code = run_module("simcortexpp.deform.eval", overrides or [])
+    raise typer.Exit(code)
+
+if __name__ == "__main__":
+    app()

simcortexpp/configs/deform/eval.yaml

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+user_config: null
+
+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+  split_name: test
+  session_label: "01"
+  space: "MNI152"
+
+  # Stage 1 roots (GT surfaces)
+  roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+outputs:
+  # Stage 4 prediction roots (deformed surfaces)
+  pred_roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-deform-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-deform-0.1
+
+  out_dir: /project/hippocampus/common/kaveh/workspace/scpp-runs/deform/exp01_hcpya+oasis1/eval_test
+
+eval:
+  pred_desc: "deform"     # matches inference naming: desc-deform
+  device: "cuda:0"
+  n_chamfer: 150000
+  n_assd_hd: 150000
+  log_level: "INFO"
+
+hydra:
+  run:
+    dir: ${outputs.out_dir}
+  output_subdir: null
+  job:
+    chdir: false

simcortexpp/configs/deform/inference.yaml

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+user_config: null
+
+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+  split_name: test
+  session_label: "01"
+  space: "MNI152"
+
+  # Where T1 + GT FS surfaces live (Stage 1 outputs)
+  roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+  # Where init surfaces + ribbon_prob live (Stage 3 outputs)
+  initsurf_roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-initsurf-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-initsurf-0.1
+
+  surface_name: ["lh_pial", "lh_white", "rh_pial", "rh_white"]
+
+  prob_clip_min: 0.0
+  prob_clip_max: 1.0
+  prob_gamma: 1.0
+  add_prob_grad: false
+
+inference:
+  device: "cuda:0"
+  batch_size: 1
+  num_workers: 2
+  log_level: "INFO"
+  overwrite: true
+
+model:
+  ckpt_path: /project/hippocampus/common/kaveh/workspace/scpp-runs/deform/exp01_hcpya+oasis1/checkpoints/deform_best_rmse.pth
+  strict_load: true
+
+  c_in: 2
+  sigma: 1
+  n_steps: 8
+  inshape: [184, 224, 184]
+  c_hid: [8, 16, 32, 64, 128, 128]
+
+  geom_ratio: 0.5
+  geom_depth: 6
+  gn_groups: 8
+  gate_init: -3.0
+
+outputs:
+  out_roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-deform-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-deform-0.1
+
+  log_dir: /project/hippocampus/common/kaveh/workspace/scpp-runs/deform/exp01_hcpya+oasis1/logs_infer_test
+
+hydra:
+  run:
+    dir: ${outputs.log_dir}
+  output_subdir: null
+  job:
+    chdir: false

simcortexpp/configs/deform/train.yaml

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+user_config: null
+
+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+  train_split_name: train
+  val_split_name: val
+
+  session_label: "01"
+  space: "MNI152"
+
+  roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+  initsurf_roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-initsurf-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-initsurf-0.1
+
+  surface_name: ["lh_pial", "lh_white", "rh_pial", "rh_white"]
+
+  prob_clip_min: 0.0
+  prob_clip_max: 1.0
+  prob_gamma: 1.0
+  add_prob_grad: false
+
+  aug_prob: 0.30
+  aug_rot_range_deg: 5.0
+  aug_scale_range: 0.03
+  aug_trans_range_mm: 2.0
+
+trainer:
+  seed: 2025
+  img_batch_size: 1
+  grad_accum_steps: 4
+  num_epochs: 500
+  validation_interval: 5
+  collision_interval: 50
+
+  learning_rate: 1.0e-4
+  weight_decay: 5.0e-5
+
+  points_per_image: 150000
+  val_points_per_image: 100000
+  num_workers: 4
+  log_level: INFO
+  mesh_chunk: 4
+  grad_clip_norm: 1.0
+
+  scheduler_patience: 2
+  scheduler_factor: 0.5
+  scheduler_min_lr: 1.0e-6
+  scheduler_threshold_mm: 0.0
+  scheduler_threshold_mode: rel
+  scheduler_cooldown: 0
+
+  early_stop_patience: 12
+  early_stop_min_delta_mm: 0.0003
+
+model:
+  sigma: 1
+  n_steps: 8
+  inshape: [184, 224, 184]
+  c_hid: [8, 16, 32, 64, 128, 128]
+  c_in: 2
+
+  geom_ratio: 0.5
+  geom_depth: 6
+  gn_groups: 8
+  gate_init: -3.0
+
+  init_ckpt: ""
+  init_strict: true
+
+objective:
+  chamfer_weight: 1.0
+  edge_loss_weight: 0.3
+  normal_weight: 0.3
+  reg_warmup_epochs: 10
+
+  hd_weight: 5.0
+  hd_p: 0.01
+  hd_lambda_mm: 0.6
+  hd_points: 60000
+
+  pial_lr_hd_weight: 0.5
+  pial_lr_hd_p: 0.001
+  pial_lr_hd_lambda_mm: 0.6
+  pial_lr_hd_points: 25000
+
+outputs:
+  root: /project/hippocampus/common/kaveh/workspace/scpp-runs/deform/exp01_hcpya+oasis1
+
+hydra:
+  run:
+    dir: ${outputs.root}
+  output_subdir: null
+  job:
+    chdir: false

simcortexpp/configs/initsurf/generate.yaml

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+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+  split_name: all
+  session_label: "01"
+  space: "MNI152"
+
+  # Preproc roots (where preprocessed T1 lives)
+  roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+
+  # Segmentation roots (where seg9_dseg lives)
+  seg_roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-seg-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-seg-0.1
+
+outputs:
+  out_roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-initsurf-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-initsurf-0.1
+  log_dir: /project/hippocampus/common/kaveh/workspace/scpp-runs/initsurf/exp01_hcpya+oasis1/logs_generate
+
+params:
+  gap_size: 1
+
+  sdf_sigma: 0.5
+  topo_threshold: 16.0
+  n_smooth: 2
+
+  wm_thickness: 1.0
+  wm_start_level: -0.2
+  wm_step: -0.08
+  wm_min_level: -5.0
+  wm_max_iters: 120
+
+  pial_start_level: 0.1
+  pial_step: 0.05
+  pial_max_level: 5.0
+  pial_max_iters: 120
+  pial_shrink_step: 0.05
+  pial_shrink_max_iters: 80
+
+
+hydra:
+  run:
+    dir: ${outputs.log_dir}
+  output_subdir: null
+  job:
+    chdir: false

simcortexpp/configs/seg/eval.yaml

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+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+  split_name: test
+  session_label: "01"
+  space: MNI152
+
+  roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+evaluation:
+  num_classes: 9
+  exclude_background: true
+  nsd_tolerance_vox: 1.0
+  spacing: [1.0, 1.0, 1.0]
+
+outputs:
+  pred_roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-seg-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-seg-0.1
+
+  log_dir:  /project/hippocampus/common/kaveh/workspace/scpp-runs/seg/exp01_hcpya+oasis1/logs_eval_test
+  eval_csv: /project/hippocampus/common/kaveh/workspace/scpp-runs/seg/exp01_hcpya+oasis1/metrics_test.csv
+  eval_xlsx: /project/hippocampus/common/kaveh/workspace/scpp-runs/seg/exp01_hcpya+oasis1/metrics_test.xlsx
+
+hydra:
+  run:
+    dir: ${outputs.log_dir}
+  output_subdir: null
+  job:
+    chdir: false

simcortexpp/configs/seg/inference.yaml

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+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+  split_name: test
+  session_label: "01"
+  space: "MNI152"
+  pad_mult: 16
+
+  roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+trainer:
+  device: cuda:0
+  batch_size: 2
+  num_workers: 4
+
+model:
+  in_channels: 1
+  out_channels: 9
+  ckpt_path: /project/hippocampus/common/kaveh/workspace/scpp-runs/seg/exp01_hcpya+oasis1/checkpoints/seg_best_dice.pt
+
+outputs:
+  out_roots:
+    HCP_YA: /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-seg-0.1
+    OASIS1: /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-seg-0.1
+
+  log_dir: /project/hippocampus/common/kaveh/workspace/scpp-runs/seg/exp01_hcpya+oasis1/logs_infer_test
+
+
+hydra:
+  run:
+    dir: ${outputs.log_dir}
+  output_subdir: null
+  job:
+    chdir: false

simcortexpp/configs/seg/train.yaml

@@ -0,0 +1,42 @@
+dataset:
+  split_file: /project/hippocampus/common/kaveh/workspace/datasets/splits/dataset_split.csv
+
+  roots:
+    HCP_YA:  /project/hippocampus/common/kaveh/workspace/datasets/hcpya-u100/derivatives/scpp-preproc-0.1
+    OASIS1:  /project/hippocampus/common/kaveh/workspace/datasets/oasis-1/derivatives/scpp-preproc-0.1
+
+  train_split: train
+  val_split: val
+  session_label: "01"
+  space: "MNI152"
+  pad_mult: 16
+  augment: true
+
+
+trainer:
+  device: cuda:0
+  num_epochs: 500
+  learning_rate: 1e-4
+  batch_size: 6
+  num_workers: 4
+  validation_interval: 15
+  dice_weight: 1.0
+  use_ddp: true
+  data_parallel: false
+
+model:
+  in_channels: 1
+  out_channels: 9
+
+outputs:
+  root: /project/hippocampus/common/kaveh/workspace/scpp-runs/seg/exp01_hcpya+oasis1
+  log_dir:  ${outputs.root}/logs_train
+  ckpt_dir: ${outputs.root}/checkpoints
+
+
+hydra:
+  run:
+    dir: ${outputs.log_dir}
+  output_subdir: null
+  job:
+    chdir: false