Fix post-merge errors, missing docstrings, and docs build config

Merge introduced new functions and a renamed parameter that broke ruff:
- dicom_extract.py: rename parameter hunk → chunk (was chunk in body,
  causing F821 undefined name + ARG001 unused arg)
- dicom_extract.py: add docstring + return type to dicom_to_nifti_multiframe_2d
- elastic_deform.py (new file): fix D212/D415 docstring format, add
  docstrings and return types for pad() and get_random_deform_parameter()
- nii_wrapper.py: add docstring + return types for from_deepali,
  erode_msk_euclid, dilate_msk_euclid
- np_utils.py: fix D205/D415 and add return types for np_erode_msk_euclid,
  np_dilate_msk_euclid
- vert_constants.py: add docstring + return type for Full_Body_Instance.feet
- log_file.py: add docstrings for warning() and error() methods

Fix ReadTheDocs docs build: extra_requirements=[docs] requires a pip extra
in pyproject.toml, but docs is only a Poetry optional group. Switch to
build.jobs.post_install to install mkdocs packages directly instead.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Hendrik-code

.readthedocs.yml

@@ -4,6 +4,9 @@ build:
   os: ubuntu-24.04
   tools:
     python: "3.12"
+  jobs:
+    post_install:
+      - pip install "mkdocs>=1.6" "mkdocs-material>=9.5" "mkdocstrings[python]>=0.25"
 
 mkdocs:
   configuration: mkdocs.yml
@@ -12,5 +15,3 @@ python:
   install:
     - method: pip
       path: .
-      extra_requirements:
-        - docs

CLAUDE.md

@@ -0,0 +1,95 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+TPTBox is a Python package for processing BIDS-compliant medical imaging datasets (CT, MRI), with a focus on torso/spine analysis. It provides NIfTI I/O, reorientation/resampling, Points of Interest (POI) computation for vertebrae, 2D/3D snapshots, registration, and segmentation integrations (SPINEPS, nnU-Net).
+
+## Commands
+
+### Installation
+```bash
+pip install poetry
+poetry install --with dev
+```
+
+### Running Tests
+```bash
+# All tests
+pytest unit_tests/
+
+# Single test file
+pytest unit_tests/test_nii.py
+
+# Single test function
+pytest unit_tests/test_nii.py::test_function_name
+
+# With coverage
+coverage run --source=TPTBox -m pytest unit_tests/
+```
+
+### Linting & Formatting
+```bash
+# Lint (auto-fix where possible)
+ruff check . --fix
+
+# Format
+ruff format .
+
+# Both (mirrors pre-commit behavior)
+pre-commit run --all-files
+```
+
+### CI Linting (as run in GitHub Actions)
+```bash
+flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+```
+
+## Architecture
+
+### Core Abstractions
+
+**`NII`** (`TPTBox/core/nii_wrapper.py`) — Central class wrapping nibabel NIfTI images. Handles reorientation, resampling, affine transforms, boolean masking, and mathematical operations. Nearly all image operations in the package go through `NII`. Math operations live in `nii_wrapper_math.py` as mixins.
+
+**`POI`** (`TPTBox/core/poi.py`) — Points of Interest container mapping `(vertebra_id, subregion_id) → 3D coordinate`. Coordinates can be in voxel or world space. POI computation strategies live in `TPTBox/core/poi_fun/`.
+
+**`BIDS_FILE` / `BIDS_Global_info`** (`TPTBox/core/bids_files.py`) — BIDS dataset navigator. `BIDS_Global_info` scans a dataset root, while `BIDS_FILE` represents a single file parsed according to BIDS naming entities. Constants for BIDS key/value vocabulary are in `bids_constants.py`.
+
+**`Location` / `Vertebra_Instance`** (`TPTBox/core/vert_constants.py`) — Enum-like constants for vertebral anatomy (vertebra IDs, subregion labels). Used as keys into `POI` objects throughout the codebase.
+
+### Package Layout
+
+```
+TPTBox/
+├── core/           # NII, POI, BIDS parsing, numpy utilities, vertebra constants
+│   └── poi_fun/    # POI calculation strategies and serialization
+├── spine/          # Spine-specific: 2D snapshots, statistics (distances, angles)
+├── segmentation/   # SPINEPS integration, nnU-Net inference, defacing
+├── registration/   # ANTs rigid/deformable, DeepALI deep learning registration
+├── mesh3D/         # 3D mesh generation and rendering from segmentations
+├── stitching/      # Multi-station image stitching
+└── logger/         # Logging infrastructure (Logger, Print_Logger, No_Logger)
+```
+
+Public API is re-exported from `TPTBox/__init__.py`. All major classes and utility functions are importable directly from `TPTBox`.
+
+### Key Relationships
+
+- `NII` + `POI` are used together constantly: compute POIs from segmentation `NII`s, then use POIs to guide further processing.
+- `BIDS_Global_info` iterates subjects/sessions; each subject has a `Subject_Container` with `BIDS_FILE` entries; `BIDS_FILE.get_nii()` returns a `NII`.
+- `vert_constants.py` defines the shared label space (`Location` enum) that ties segmentation labels to POI keys to snapshot rendering.
+- External tool integrations (SPINEPS, nnU-Net, ANTs, DeepALI) are optional; their imports are guarded so the core works without them.
+
+### Test Layout
+
+Tests live in `unit_tests/` (not `TPTBox/tests/`). `TPTBox/tests/` contains test utilities and sample data (CT/MRI NIfTIs) used by the unit tests. Some generated test files are very large (>20K LOC) — they are autogenerated and should not be edited by hand.
+
+## Code Style
+
+- **Line length**: 140 characters
+- **Formatter**: Ruff (Black-compatible, double quotes)
+- **Target Python**: 3.10+ syntax, but the package supports 3.9–3.14
+- **Naming**: Ruff N-rules are largely ignored — mixed-case class/method names are acceptable in this codebase (medical domain conventions)
+- **Complexity**: McCabe max=20; research code legitimately has deep branching
+- `from __future__ import annotations` is used widely for forward references

TPTBox/core/bids_constants.py

@@ -64,6 +64,7 @@
     "FLASH",
     "VF",
     "defacemas",
+    "fluroscopy",
     "dw",
     "TB1TFL",
     "TB1RFM",
@@ -162,6 +163,8 @@
     "localizer",
     "difference",
     "labels",
+    "report",
+    "pet",
 ]
 # https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html
 formats_relaxed = [*formats, "t2", "t1", "t2c", "t1c", "mr", "snapshot", "t1dixon", "dwi", "ctb"]
@@ -220,7 +223,7 @@
     "OPT": "Ophthalmic Tomography",
     "OPV": "Ophthalmic Visual Field",
     "OSS": "Optical Surface Scan",
-    "OT": "Other ",
+    "OT": "Other",
     "PLAN": "Plan",
     "PR": "Presentation State",
     "PT": "Positron emission tomography (PET)",

TPTBox/core/bids_files.py

@@ -859,7 +859,7 @@ def rename_files(self, path: Path | str, ending: str = ".nii.gz") -> None:
             p = Path(path + "." + key)
             value.rename(p)
 
-    def symlink_files(self, path: Path | str, ending: str = ".nii.gz") -> None:
+    def symlink_files(self, path: Path | str, ending: str = ".nii.gz", exist_ok: bool = False) -> None:
         """Create symbolic links for all associated files at a new base path.
 
         Equivalent to :meth:`rename_files` but creates symlinks rather than
@@ -881,9 +881,13 @@ def symlink_files(self, path: Path | str, ending: str = ".nii.gz") -> None:
         path = path.replace(ending, "")
         for key, value in self.file.items():
             p = Path(path + "." + key)
+
             if os.path.islink(p):
                 assert Path(os.readlink(p)) == value, f"{p} exists"
                 continue
+            if exist_ok and p.exists():
+                continue
+
             os.symlink(value, p)
 
     def get_path_decomposed(self, file_type: str | None = None) -> tuple[Path, str, str, str]:
@@ -958,7 +962,7 @@ def get_changed_bids(
         auto_add_run_id: bool = False,
         additional_folder: str | None = None,
         dataset_path: str | None = None,
-        make_parent: bool = True,
+        make_parent: bool = False,
         non_strict_mode: bool = False,
     ) -> BIDS_FILE:
         """Construct a new :class:`BIDS_FILE` pointing to a derived output path.

TPTBox/core/dicom/dicom2nii_utils.py

@@ -285,6 +285,8 @@ def test_name_conflict(json_ob: dict, file: str | Path) -> bool:
     if Path(file).exists():
         with open(file) as f:
             js = json.load(f)
+            if "grid" in js:
+                del js["grid"]
         return js != json_ob
     return False