fix: refactor CLI and IO modules for improved functionality and type …

…safety

- Refactored CLI configuration to use `pydantic-settings` for better type safety and configuration management.
- Updated IO module to use a registration system for conversions between different mesh types, improving flexibility and maintainability.
- Enhanced type annotations and removed redundant code for better readability and maintainability.
- Added new modules for DICOM, Open3D, and PyVista IO operations, providing more robust support for various data formats.
- Fixed and improved various functions and methods across the codebase to ensure consistent behavior and type handling.

BREAKING CHANGE: The refactoring of the CLI and IO modules may require updates to existing scripts and configurations that rely on the previous implementation.

.cspell.json

@@ -10,13 +10,18 @@
     "confz",
     "corotated",
     "cuda",
+    "customise",
     "cyipopt",
     "cython",
+    "dcmread",
+    "denorm",
     "dicom",
     "disp",
     "dmypy",
+    "dotenv",
     "dvclive",
     "elems",
+    "fpfh",
     "frobenius",
     "gltf",
     "hstack",
@@ -53,6 +58,8 @@
     "pvtu",
     "pybuilder",
     "pycache",
+    "pydantic",
+    "pydicom",
     "pydocstyle",
     "pyenv",
     "pyflow",
@@ -67,7 +74,9 @@
     "pytetwild",
     "pytype",
     "pyvista",
+    "pyyaml",
     "qdwh",
+    "rint",
     "rtol",
     "scipy",
     "scrapy",

.ruff.toml

@@ -1,11 +1,15 @@
+builtins = ["ic"]
 fix = true
+preview = true
 show-fixes = true
 target-version = "py311"
 
 [format]
 docstring-code-format = true
 
 [lint]
+explicit-preview-rules = true
+extend-select = ["RUF022"]
 ignore = [
   "ANN",
   "ARG",
@@ -16,10 +20,9 @@ ignore = [
   "ERA",
   "FIX",
   "INP",
-  "ISC",
+  "N802",
   "N803",
   "N806",
-  "PD008",
   "PLR09",
   "PLR2004",
   "RET504",
@@ -34,6 +37,7 @@ select = ["ALL"]
 "jax.typing" = "jxt"
 "numpy.typing" = "npt"
 "pyvista" = "pv"
+"subprocess" = "sp"
 "taichi" = "ti"
 "trimesh" = "tm"
 

.vscode/settings.json

@@ -1,24 +1,23 @@
 {
-	"files.exclude": {
-		"**/__pycache__/": true,
-		"**/.pixi/": true,
-		"**/.pytest_cache/": true,
-		"**/*.benchmarks/": true,
-		"**/*.cache/": true,
-		"**/*.egg-info/": true,
-		"**/*.ruff_cache/": true
-	},
-	"python.analysis.diagnosticMode": "workspace",
-	"python.analysis.include": ["src"],
-	"python.testing.pytestArgs": ["src/tests/"],
-	"python.testing.pytestEnabled": true,
-	"python.testing.unittestEnabled": false,
-	"yaml.customTags": [
-		"!ENV scalar",
-		"!ENV sequence",
-		"!relative scalar",
-		"tag:yaml.org,2002:python/name:material.extensions.emoji.to_svg",
-		"tag:yaml.org,2002:python/name:material.extensions.emoji.twemoji",
-		"tag:yaml.org,2002:python/name:pymdownx.superfences.fence_code_format"
-	]
+  "files.exclude": {
+    "**/__pycache__/": true,
+    "**/.pixi/": true,
+    "**/.pytest_cache/": true,
+    "**/*.benchmarks/": true,
+    "**/*.cache/": true,
+    "**/*.egg-info/": true,
+    "**/*.ruff_cache/": true
+  },
+  "python.analysis.diagnosticMode": "workspace",
+  "python.testing.pytestArgs": ["src/tests/"],
+  "python.testing.pytestEnabled": true,
+  "python.testing.unittestEnabled": false,
+  "yaml.customTags": [
+    "!ENV scalar",
+    "!ENV sequence",
+    "!relative scalar",
+    "tag:yaml.org,2002:python/name:material.extensions.emoji.to_svg",
+    "tag:yaml.org,2002:python/name:material.extensions.emoji.twemoji",
+    "tag:yaml.org,2002:python/name:pymdownx.superfences.fence_code_format"
+  ]
 }

exp/2024/2024-08-07-constitutive/src/plot/curve.py → exp/2024/08/07/constitutive/src/plot/curve.py

@@ -16,7 +16,7 @@
     import pyvista as pv
 
 
-def E_nu_to_lambda_mu(E: float, nu: float) -> tuple[float, float]:  # noqa: N802, N803
+def E_nu_to_lambda_mu(E: float, nu: float) -> tuple[float, float]:
     lambda_: float = E * nu / ((1 + nu) * (1 - 2 * nu))
     mu: float = E / (2 * (1 + nu))
     return lambda_, mu

exp/2024/09/01/real-data/src/prepare.py

@@ -3,7 +3,6 @@
 import numpy as np
 import pyvista as pv
 from icecream import ic
-from sympy import inverse_laplace_transform
 
 import mkit
 from mkit.typing import StrPath

exp/2024/09/01/register/src/hello.py

@@ -1,7 +1,4 @@
-from typing import Any
 
-import numpy as np
-import numpy.typing as npt
 import pyvista as pv
 from icecream import ic
 

exp/2024/09/12/organize-ct/src/main.py

@@ -0,0 +1,90 @@
+import collections
+import concurrent.futures
+import shutil
+from pathlib import Path
+from typing import Literal
+
+import pydantic
+import pydicom
+
+import mkit
+
+
+class CLIConfig(mkit.cli.CLIBaseConfig):
+    raw: Path
+    output: Path
+
+
+class Acquisition(pydantic.BaseModel):
+    age: str
+    birth_date: str
+    date: str
+    id: str
+    name: str
+    sex: Literal["F", "M"]
+    time: str
+
+
+class Patient(pydantic.BaseModel):
+    acquisitions: list[Acquisition]
+    birth_date: str
+    id: str
+    name: str
+    sex: Literal["F", "M"]
+
+
+class Dataset(pydantic.BaseModel):
+    patients: dict[str, Patient]
+
+
+def extract_meta(data: pydicom.FileDataset) -> Acquisition:
+    return Acquisition(
+        age=data["PatientAge"].value,
+        birth_date=data["PatientBirthDate"].value,
+        date=data["AcquisitionDate"].value,
+        id=data["PatientID"].value,
+        name=str(data["PatientName"].value),
+        sex=data["PatientSex"].value,
+        time=data["AcquisitionTime"].value,
+    )
+
+
+def process_acquisition(dirfile_fpath: Path, output_dir: Path) -> Acquisition:
+    dirfile: pydicom.FileDataset = pydicom.dcmread(dirfile_fpath)
+    seq: pydicom.DataElement = dirfile["DirectoryRecordSequence"]
+    file_id: pydicom.DataElement = seq[0]["ReferencedFileID"]
+    record_fpath: Path = dirfile_fpath.with_name(file_id[-1])
+    record: pydicom.FileDataset = pydicom.dcmread(record_fpath)
+    meta: Acquisition = extract_meta(record)
+    ic(meta)
+    dpath: Path = output_dir / meta.id / meta.date
+    dpath.mkdir(parents=True, exist_ok=True)
+    shutil.copytree(dirfile_fpath.parent, dpath, dirs_exist_ok=True)
+    return meta
+
+
+@mkit.cli.auto_run
+def main(cfg: CLIConfig) -> None:
+    patients: dict[str, list[Acquisition]] = collections.defaultdict(list)
+    with concurrent.futures.ThreadPoolExecutor() as executor:
+        futures: list[concurrent.futures.Future[Acquisition]] = [
+            executor.submit(process_acquisition, fpath, cfg.output)
+            for fpath in cfg.raw.rglob("DIRFILE")
+        ]
+        for future in concurrent.futures.as_completed(futures):
+            meta: Acquisition = future.result()
+            patients[meta.id].append(meta)
+    dataset = Dataset(patients={})
+    for id_, acquisitions in patients.items():
+        acquisitions.sort(key=lambda x: x.date)
+        fpath: Path = cfg.output / id_ / "patient.json"
+        patient: Patient = Patient(
+            acquisitions=acquisitions,
+            birth_date=acquisitions[0].birth_date,
+            id=id_,
+            name=acquisitions[0].name,
+            sex=acquisitions[0].sex,
+        )
+        fpath.write_text(patient.model_dump_json())
+        dataset.patients[id_] = patient
+    (cfg.output / "dataset.json").write_text(dataset.model_dump_json())

exp/2024/09/12/organize-ct/src/read-dataset.py

@@ -0,0 +1,12 @@
+from pathlib import Path
+
+import mkit
+
+
+class CLIConfig(mkit.cli.CLIBaseConfig):
+    dpath: Path
+
+
+@mkit.cli.auto_run
+def main(cfg: CLIConfig) -> None:
+    dataset = mkit.io.cfg.dpath

exp/2024/09/12/registration/src/global.py

@@ -0,0 +1,60 @@
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import numpy as np
+import pyvista as pv
+
+import mkit
+import mkit.typing.numpy as nt
+from mkit.typing import StrPath
+
+if TYPE_CHECKING:
+    import open3d as o3d
+
+    from mkit.ops.registration._global._result import GlobalRegistrationResult
+
+
+class Config(mkit.cli.BaseConfig):
+    template: Path
+
+
+def read_obj(fpath: StrPath) -> pv.PolyData:
+    fpath: Path = Path(fpath)
+    group_dup: list[str] = []
+    for line in mkit.utils.strip_comments(fpath.read_text()):
+        if line.startswith("g"):
+            name: str
+            _, name = line.split()
+            group_dup.append(name)
+    group_uniq: list[str] = list(set(group_dup))
+    dup_to_uniq: dict[str, int] = {name: i for i, name in enumerate(group_uniq)}
+    mesh: pv.PolyData = pv.read(fpath)
+    group_id: nt.IN = mkit.math.numpy.cast(mesh.cell_data["GroupIds"], int)
+    group_id = np.asarray([dup_to_uniq[group_dup[i]] for i in group_id])
+    mesh.cell_data["GroupIds"] = group_id
+    mesh.field_data["GroupNames"] = group_uniq
+    return mesh
+
+
+@mkit.cli.auto_run()
+def main(cfg: Config) -> None:
+    if False:
+        demo = o3d.data.DemoICPPointClouds()
+        source: o3d.geometry.PointCloud = o3d.io.read_point_cloud(demo.paths[0])
+        source_pv: pv.PolyData = pv.wrap(np.asarray(source.points))
+        target: o3d.geometry.PointCloud = o3d.io.read_point_cloud(demo.paths[1])
+        target_pv: pv.PolyData = pv.wrap(np.asarray(target.points))
+        ic(0.05 / source_pv.length)
+        ic(0.05 / target_pv.length)
+        return
+    source: pv.PolyData = read_obj(cfg.template)
+    target: pv.PolyData = mkit.ext.sculptor.get_template_skull()
+    source.save("data/source.vtp")
+    target.save("data/target.vtp")
+    result: GlobalRegistrationResult = mkit.ops.registration.global_registration(
+        source, target
+    )
+    source.transform(result.transform, inplace=True)
+    ic(np.unique(source.cell_data["GroupIds"]))
+    ic(source.field_data["GroupNames"])
+    source.save("data/result.vtp")

exp/2024/09/12/registration/src/rigid.py

@@ -0,0 +1,30 @@
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import numpy as np
+
+import mkit
+
+if TYPE_CHECKING:
+    import pyvista as pv
+
+    from mkit.ops.registration.rigid._result import RigidRegistrationResult
+
+
+class Config(mkit.cli.BaseConfig):
+    template: Path
+
+
+@mkit.cli.auto_run()
+def main(cfg: Config) -> None:
+    source: pv.PolyData = mkit.io.pyvista.read_poly_data(cfg.template)
+    target: pv.PolyData = mkit.ext.sculptor.get_template_skull()
+    source.save("data/source.vtp")
+    target.save("data/target.vtp")
+    result: RigidRegistrationResult = mkit.ops.registration.rigid_registration(
+        source, target
+    )
+    source.transform(result.transform, inplace=True)
+    ic(np.unique(source.cell_data["GroupIds"]))
+    ic(source.field_data["GroupNames"])
+    source.save("data/result.vtp")

mkdocs.yaml

@@ -27,8 +27,8 @@ theme:
     - navigation.instant.prefetch
     - navigation.instant.progress
     - navigation.path
-    - navigation.prune
-    # - navigation.sections
+    # - navigation.prune
+    - navigation.sections
     - navigation.tabs
     - navigation.tabs.sticky
     - navigation.top
@@ -87,14 +87,15 @@ plugins:
             - https://trimesh.org/objects.inv
           options:
             # General
-            show_inheritance_diagram: true
+            show_source: false
             # Headings
             show_symbol_type_heading: true
             show_symbol_type_toc: true
             # Members
             inherited_members: true
             filters:
               - "!^_[^_]"
+              - "!__all__"
             summary: true
             # Docstrings
             docstring_section_style: list
@@ -105,6 +106,6 @@ plugins:
             signature_crossrefs: true
 
 watch:
-  - docs
-  - src/mkit
+  - docs/
+  - src/mkit/
   - tools/gen-ref-pages.py