brkraw 0.5.5__py3-none-any.whl → 0.5.7__py3-none-any.whl

brkraw/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-__version__ = '0.5.5'
+__version__ = '0.5.7'
 from .apps.loader import BrukerLoader
 
 

brkraw/apps/addon/dependencies.py

@@ -17,11 +17,23 @@ RULE_KEYS = {"info_spec", "metadata_spec", "converter_hook"}
 _SPEC_EXTS = (".yaml", ".yml")
 
 
-def warn_dependencies(target: Path, *, kind: str, root: Optional[Union[str, Path]]) -> bool:
+def warn_dependencies(
+    target: Path,
+    *,
+    kind: str,
+    root: Optional[Union[str, Path]],
+    ignore_rules_dir: Optional[Path] = None,
+    ignore_specs_dir: Optional[Path] = None,
+) -> bool:
     paths = config_core.paths(root=root)
     warned = False
     if kind == "spec":
-        used_by_rules = rules_using_spec(target.name, paths.rules_dir)
+        used_by_rules = rules_using_spec(
+            target,
+            paths.rules_dir,
+            root=paths.root,
+            ignore_dir=ignore_rules_dir,
+        )
         if used_by_rules:
             logger.warning(
                 "Spec %s is referenced by rules: %s",
@@ -29,7 +41,11 @@ def warn_dependencies(target: Path, *, kind: str, root: Optional[Union[str, Path
                 ", ".join(sorted(used_by_rules)),
             )
             warned = True
-        included_by = specs_including_spec(target.name, paths.specs_dir)
+        included_by = specs_including_spec(
+            target,
+            paths.specs_dir,
+            ignore_dir=ignore_specs_dir,
+        )
         if included_by:
             logger.warning(
                 "Spec %s is included by: %s",
@@ -54,12 +70,34 @@ def warn_dependencies(target: Path, *, kind: str, root: Optional[Union[str, Path
     return warned
 
 
-def rules_using_spec(spec_name: str, rules_dir: Path) -> Set[str]:
+def _is_under(path: Path, base: Optional[Path]) -> bool:
+    if base is None:
+        return False
+    try:
+        path.relative_to(base)
+    except ValueError:
+        return False
+    return True
+
+
+def rules_using_spec(
+    target: Union[str, Path],
+    rules_dir: Path,
+    *,
+    root: Optional[Union[str, Path]] = None,
+    ignore_dir: Optional[Path] = None,
+) -> Set[str]:
     used_by: Set[str] = set()
     if not rules_dir.exists():
         return used_by
+    if isinstance(target, Path):
+        target_path = target.resolve()
+    else:
+        target_path = None
     files = list(rules_dir.rglob("*.yaml")) + list(rules_dir.rglob("*.yml"))
     for path in files:
+        if _is_under(path, ignore_dir):
+            continue
         data = yaml.safe_load(path.read_text(encoding="utf-8"))
         if not isinstance(data, dict):
             continue
@@ -70,17 +108,46 @@ def rules_using_spec(spec_name: str, rules_dir: Path) -> Set[str]:
                 if not isinstance(item, dict):
                     continue
                 use = item.get("use")
-                if isinstance(use, str) and Path(use).name == spec_name:
+                if not isinstance(use, str):
+                    continue
+                if target_path is None:
+                    if Path(use).name == str(target):
+                        used_by.add(path.name)
+                    continue
+                if root is None:
+                    continue
+                version = item.get("version") if isinstance(item.get("version"), str) else None
+                try:
+                    resolved = resolve_spec_reference(
+                        use,
+                        category=key,
+                        version=version,
+                        root=root,
+                    )
+                except Exception:
+                    continue
+                if resolved.resolve() == target_path:
                     used_by.add(path.name)
     return used_by
 
 
-def specs_including_spec(spec_name: str, specs_dir: Path) -> Set[str]:
+def specs_including_spec(
+    target: Union[str, Path],
+    specs_dir: Path,
+    *,
+    ignore_dir: Optional[Path] = None,
+) -> Set[str]:
     included_by: Set[str] = set()
     if not specs_dir.exists():
         return included_by
+    if isinstance(target, Path):
+        target_path = target.resolve()
+    else:
+        target_path = None
     files = list(specs_dir.rglob("*.yaml")) + list(specs_dir.rglob("*.yml"))
     for path in files:
+        if _is_under(path, ignore_dir):
+            continue
         data = yaml.safe_load(path.read_text(encoding="utf-8"))
         if not isinstance(data, dict):
             continue
@@ -92,8 +159,17 @@ def specs_including_spec(spec_name: str, specs_dir: Path) -> Set[str]:
                 include_list = [include]
             elif isinstance(include, list) and all(isinstance(item, str) for item in include):
                 include_list = include
-        if any(Path(item).name == spec_name for item in include_list):
-            included_by.add(path.name)
+        for item in include_list:
+            inc_path = Path(item)
+            if not inc_path.is_absolute():
+                inc_path = (path.parent / inc_path).resolve()
+            if target_path is None:
+                if inc_path.name == str(target):
+                    included_by.add(path.name)
+                    break
+            elif inc_path == target_path:
+                included_by.add(path.name)
+                break
     return included_by
 
 

brkraw/apps/hook/core.py

@@ -150,12 +150,18 @@ def uninstall_hook(
         "transforms": [],
     }
     root_path = config_core.resolve_root(root)
+    namespace = entry.get("namespace") if isinstance(entry, dict) else None
     for kind in ("specs", "pruner_specs", "rules", "transforms"):
         for relpath in entry.get(kind, []) if isinstance(entry, dict) else []:
             target_path = root_path / relpath
             if not target_path.exists():
                 continue
-            if _has_dependencies(target_path, kind, root=root_path) and not force:
+            if _has_dependencies(
+                target_path,
+                kind,
+                root=root_path,
+                namespace=namespace,
+            ) and not force:
                 raise RuntimeError("Dependencies found; use --force to remove.")
             target_path.unlink()
             removed[kind].append(relpath)
@@ -587,9 +593,22 @@ def _has_dependencies(
     kind: str,
     *,
     root: Optional[Union[str, Path]],
+    namespace: Optional[str] = None,
 ) -> bool:
     try:
-        return addon_deps.warn_dependencies(target, kind=_kind_to_remove(kind), root=root)
+        ignore_rules_dir = None
+        ignore_specs_dir = None
+        if namespace:
+            paths = config_core.paths(root=root)
+            ignore_rules_dir = paths.rules_dir / namespace
+            ignore_specs_dir = paths.specs_dir / namespace
+        return addon_deps.warn_dependencies(
+            target,
+            kind=_kind_to_remove(kind),
+            root=root,
+            ignore_rules_dir=ignore_rules_dir,
+            ignore_specs_dir=ignore_specs_dir,
+        )
     except Exception:
         return False
 

brkraw/apps/loader/core.py

@@ -565,7 +565,6 @@ class BrukerLoader:
 
             if scope == 'scan':
                 if not as_dict:
-                    config_core.configure_logging(root=base, stream=sys.stdout)
                     text = format_info_tables(
                         {"Scan(s)": scan_info},
                         width=width,
@@ -574,7 +573,7 @@ class BrukerLoader:
                         scan_transpose=scan_transpose,
                         float_decimals=float_decimals,
                     )
-                    logger.info("%s", text)
+                    print(text)
                     return None
                 return scan_info
         
@@ -586,19 +585,17 @@ class BrukerLoader:
         
         if scope == 'study':
             if not as_dict:
-                config_core.configure_logging(root=base, stream=sys.stdout)
                 text = format_info_tables(
                     study_info,
                     width=width,
                     float_decimals=float_decimals,
                 )
-                logger.info("%s", text)
+                print(text)
                 return None
             return study_info
         
         study_info['Scan(s)'] = scan_info
         if not as_dict:
-            config_core.configure_logging(root=base, stream=sys.stdout)
             text = format_info_tables(
                 study_info,
                 width=width,
@@ -607,7 +604,7 @@ class BrukerLoader:
                 scan_transpose=scan_transpose,
                 float_decimals=float_decimals,
             )
-            logger.info("%s", text)
+            print(text)
             return None
         return study_info
 

brkraw/apps/loader/info/scan.yaml

@@ -56,6 +56,10 @@ FOV (mm):
     - file: method
       key: PVM_Fov
   transform: convert_to_list
+Num Slices:
+  sources:
+    - file: acqp
+      key: NSLICES
 NumSlicePack:
   sources:
     - file: method

brkraw/apps/loader/info/study.yaml

@@ -5,7 +5,7 @@ study:
     description: "Study-level info mapping for Bruker datasets."
     category: "info_spec"
     transforms_source: "transform.py"
-  Study.Opperator:
+  Study.Operator:
     sources:
       - file: subject
         key: SUBJECT_referral
@@ -91,7 +91,7 @@ scan:
     description: "Scan-level fallback info mapping for Bruker datasets."
     category: "info_spec"
     transforms_source: "transform.py"
-  Study.Opperator:
+  Study.Operator:
     sources:
       - file: visu_pars
         key: VisuStudyReferringPhysician

brkraw/apps/loader/types.py

@@ -28,10 +28,10 @@ if TYPE_CHECKING:
     from ...resolver.nifti import Nifti1HeaderContents, XYZUNIT, TUNIT
 
 
-InfoScope = Literal['full', 'study', 'scan']
+InfoScope: TypeAlias = Literal['full', 'study', 'scan']
 Dataobjs = Optional[Union[NDArray, Tuple[NDArray, ...]]]
 Affines = Optional[Union[NDArray, Tuple[NDArray, ...]]]
-AffineSpace = Literal["raw", "scanner", "subject_ras"]
+AffineSpace: TypeAlias = Literal["raw", "scanner", "subject_ras"]
 ConvertedObj = Optional[Union["ToFilename", Tuple["ToFilename", ...]]]
 Metadata = Optional[Union[Dict, Tuple[Optional[Dict], ...]]]
 HookArgs = Optional[Mapping[str, Mapping[str, Any]]]

brkraw/cli/commands/convert.py

@@ -12,7 +12,7 @@ import logging
 import os
 import re
 from pathlib import Path
-from typing import Any, Mapping, Optional, Dict, List, Tuple, cast, get_args
+from typing import Any, Mapping, Optional, Dict, List, Tuple, Sequence, cast, get_args
 
 import numpy as np
 from brkraw.cli.utils import load
@@ -387,6 +387,8 @@ def cmd_convert(args: argparse.Namespace) -> int:
             for path in output_paths:
                 reserved_paths.add(path)
 
+            _ensure_output_dirs(output_paths)
+
             sidecar_meta = None
             if args.sidecar:
                 sidecar_meta = loader.get_metadata(
@@ -397,12 +399,10 @@ def cmd_convert(args: argparse.Namespace) -> int:
 
             if args.no_convert:
                 for path in output_paths:
-                    path.parent.mkdir(parents=True, exist_ok=True)
                     _write_sidecar(path, sidecar_meta)
                     total_written += 1
             else:
                 for path, obj in zip(output_paths, nii_list):
-                    path.parent.mkdir(parents=True, exist_ok=True)
                     obj.to_filename(str(path))
                     logger.info("Wrote NIfTI: %s", path)
                     total_written += 1
@@ -713,6 +713,15 @@ def _parse_hook_args(values: List[str]) -> Dict[str, Dict[str, Any]]:
     return parsed
 
 
+def _ensure_output_dirs(paths: Sequence[Path]) -> None:
+    for path in paths:
+        try:
+            path.parent.mkdir(parents=True, exist_ok=True)
+        except OSError as exc:
+            logger.error("Failed to create output directory %s: %s", path.parent, exc)
+            raise
+
+
 def _uses_counter_tag(
     *,
     layout_template: Optional[str],

brkraw/cli/commands/hook.py

@@ -274,7 +274,8 @@ def cmd_preset(args: argparse.Namespace) -> int:
         return 2
     preset = _infer_hook_preset(entry)
     payload = {"hooks": {args.target: preset}}
-    text = yaml.safe_dump(payload, sort_keys=False)
+    normalized = _normalize_yaml_payload(payload)
+    text = yaml.safe_dump(normalized, sort_keys=False)
     if args.output:
         Path(args.output).expanduser().write_text(text, encoding="utf-8")
         logger.info("Wrote preset: %s", args.output)
@@ -283,6 +284,18 @@ def cmd_preset(args: argparse.Namespace) -> int:
     return 0
 
 
+def _normalize_yaml_payload(value: Any) -> Any:
+    if isinstance(value, Path):
+        return str(value)
+    if dataclasses.is_dataclass(value) and not isinstance(value, type):
+        return _normalize_yaml_payload(dataclasses.asdict(value))
+    if isinstance(value, dict):
+        return {key: _normalize_yaml_payload(item) for key, item in value.items()}
+    if isinstance(value, (list, tuple, set)):
+        return [_normalize_yaml_payload(item) for item in value]
+    return value
+
+
 def register(subparsers: argparse._SubParsersAction) -> None:  # type: ignore[name-defined]
     hook_parser = subparsers.add_parser(
         "hook",

brkraw/cli/commands/info.py

@@ -39,7 +39,7 @@ def cmd_info(args: argparse.Namespace) -> int:
         width=width,
     )
     if text is not None:
-        logger.info("%s", text)
+        print(text)
     return 0
 
 

brkraw/cli/commands/prune.py

@@ -97,7 +97,7 @@ def register(subparsers: argparse._SubParsersAction) -> None:  # type: ignore[na
         "--output",
         dest="output",
         type=str,
-        help="Output zip path (default: <input>_pruned.*).",
+        help="Output zip path (default: ./<root_name>.zip when omitted).",
     )
     prune_parser.add_argument(
         "--no-validate",

brkraw/cli/utils.py

@@ -7,6 +7,7 @@ from __future__ import annotations
 
 import itertools
 import logging
+import sys
 import threading
 import time
 from contextlib import contextmanager
@@ -26,7 +27,7 @@ def spinner(prefix: str = "Loading") -> Iterator[None]:
     Yields:
         None.
     """
-    if logger.isEnabledFor(logging.DEBUG):
+    if logger.isEnabledFor(logging.DEBUG) or not sys.stdout.isatty():
         yield
         return
 
@@ -35,7 +36,11 @@ def spinner(prefix: str = "Loading") -> Iterator[None]:
 
     def run() -> None:
         while not stop_event.is_set():
-            print(f"\r{prefix} {next(seq)}", end="", flush=True)
+            try:
+                print(f"\r{prefix} {next(seq)}", end="", flush=True)
+            except BrokenPipeError:
+                stop_event.set()
+                break
             time.sleep(0.08)
 
     thread = threading.Thread(target=run, daemon=True)
@@ -45,7 +50,10 @@ def spinner(prefix: str = "Loading") -> Iterator[None]:
     finally:
         stop_event.set()
         thread.join()
-        print("\r" + " " * (len(prefix) + 2) + "\r", end="", flush=True)
+        try:
+            print("\r" + " " * (len(prefix) + 2) + "\r", end="", flush=True)
+        except BrokenPipeError:
+            pass
 
 
 def load(path, *, prefix: str = "Loading") -> BrukerLoader:

brkraw/resolver/affine.py

@@ -1,6 +1,13 @@
 from __future__ import annotations
-from typing import Optional, Union, TypedDict, Tuple, Literal, List, Any
-from typing import cast, TYPE_CHECKING
+from typing import Optional, Union, TypedDict, Tuple, Literal, List, Any, TYPE_CHECKING
+from typing import cast
+if TYPE_CHECKING:
+    from typing_extensions import TypeAlias
+else:
+    try:
+        from typing import TypeAlias
+    except ImportError:  # pragma: no cover - fallback for Python 3.8
+        from typing_extensions import TypeAlias
 from .helpers import get_file, get_reco, return_alt_val_if_none
 import logging
 import numpy as np
@@ -11,8 +18,8 @@ if TYPE_CHECKING:
     from ..dataclasses import Scan, Reco
     from ..core.parameters import Parameters
 
-SubjectType = Literal["Biped", "Quadruped", "Phantom", "Other", "OtherAnimal"]
-SubjectPose = Literal[
+SubjectType: TypeAlias = Literal["Biped", "Quadruped", "Phantom", "Other", "OtherAnimal"]
+SubjectPose: TypeAlias = Literal[
     "Head_Supine", "Head_Prone", "Head_Left", "Head_Right",
     "Foot_Supine", "Foot_Prone", "Foot_Left", "Foot_Right",
 ]
@@ -405,11 +412,37 @@ def resolve_matvec_and_shape(visu_pars,
         shape = np.append(shape, _num_slices)
         extent = np.append(extent, _num_slices * _slice_thickness)
     else:
-        _rotate = np.squeeze(rotate)
+        spack_slices = visu_pars.get("VisuCoreSlicePacksSlices")
+        spack_count: Optional[int] = None
+        if spack_slices is not None:
+            spack_arr = np.asarray(spack_slices)
+            if spack_arr.ndim >= 1:
+                spack_count = int(spack_arr.shape[0])
+                if spack_count == 0:
+                    spack_count = None
+
+        def _select_pack_row(arr: np.ndarray, *, width: int, name: str) -> np.ndarray:
+            arr = np.asarray(arr, dtype=float)
+            if arr.ndim == 1:
+                if arr.size != width:
+                    raise ValueError(f"{name} has shape {arr.shape}, expected ({width},)")
+                return arr
+            if arr.ndim != 2 or arr.shape[1] != width:
+                raise ValueError(f"{name} has shape {arr.shape}, expected (*, {width})")
+            if spack_count is None or spack_count == 1:
+                return arr[0, :]
+            if spack_idx < 0 or spack_idx >= arr.shape[0]:
+                raise IndexError(
+                    f"spack_idx out of range for {name}: {spack_idx} (entries: {arr.shape[0]})"
+                )
+            return arr[spack_idx, :]
+
+        _rotate = _select_pack_row(rotate, width=9, name="VisuCoreOrientation")
+        _origin = _select_pack_row(origin, width=3, name="VisuCorePosition")
         row = _rotate[0:3]
         col = _rotate[3:6]
         slc = _rotate[6:9]
-        vec = np.squeeze(origin)
+        vec = np.squeeze(_origin)
 
     rot = np.column_stack([row, col, slc])
     resols = extent / shape

brkraw/resolver/nifti.py

@@ -260,7 +260,7 @@ def resolve(
     
     if num_cycles > 1:
         time_step = cast(float, image_info['time_per_cycle']) / 1000.0
-        num_slices = image_info['dataobj'].shape[2]
+        num_slices = cast(np.ndarray, image_info['dataobj']).shape[2]
         slice_duration = time_step / num_slices
     else:
         time_step = None

{brkraw-0.5.5.dist-info → brkraw-0.5.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brkraw
-Version: 0.5.5
+Version: 0.5.7
 Summary: Toolkit for loading Bruker Paravision datasets, mapping metadata, and exporting NIfTI
 Project-URL: Homepage, https://brkraw.github.io
 Maintainer-email: SungHo Lee <shlee@unc.edu>
@@ -49,7 +49,7 @@ Description-Content-Type: text/markdown
 
 A modular toolkit for Bruker MRI raw-data handling.
 
-BrkRaw (v0.5.5) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.7) converts raw data into standardized, neuroimaging-ready
 datasets, with extensible rules/specs and plugin hooks.
 
 - Documentation: [brkraw.github.io](https://brkraw.github.io/)
@@ -70,7 +70,7 @@ If you use BrkRaw in your research, please cite it.
 @software{brkraw,
   author = {Lee, Sung-Ho and Devenyi, Gabriel A. and Ban, Woomi and Shih, Yen-Yu Ian},
   title = {BrkRaw: A modular toolkit for Bruker MRI raw-data handling},
-  version = {0.5.5},
+  version = {0.5.7},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},

{brkraw-0.5.5.dist-info → brkraw-0.5.7.dist-info}/RECORD

@@ -1,39 +1,39 @@
-brkraw/__init__.py,sha256=NNoLZss9K8Drck-8uP0v-fmqjTX4pxmlAi1s4ZLsw20,210
+brkraw/__init__.py,sha256=6LifbJIia8iXJ8kuTt4Naq-0aVQREIB0dG0MKf-i72s,210
 brkraw/api/__init__.py,sha256=y7ZSFdF2uZK5e6ExGt3CQGg-DD5fmT0WouQiplSbwsA,3858
 brkraw/api/types.py,sha256=s11MIkHApOeREQZeIbx1zXz5R4WtYaBIVXD4s47Vnoc,672
 brkraw/apps/__init__.py,sha256=sEdA1SrY-Vu0xU1ct5Eab7vX-_IFMDip2j3FdSQVT58,170
 brkraw/apps/addon/__init__.py,sha256=fUR1QNwiaqSbkMIkPxLjKC7mJifR6HhrM8TO7lTo7Mg,531
 brkraw/apps/addon/core.py,sha256=xVlTElgOHNnoy3avNoeOudOvQSDzvuVsmGq9IVKNINc,659
-brkraw/apps/addon/dependencies.py,sha256=Hhujlqmy3DdlLfAM250r3kcl9iX2Lj4eDHBCw0TlNZo,14022
+brkraw/apps/addon/dependencies.py,sha256=C1DliuLCptgEE8-Lcg7GkQaZD9aDc80y1Fj1JPHiLvo,16037
 brkraw/apps/addon/installation.py,sha256=LeciuHv_5ENg3OjzKClgIMAg3mYs8h3VUvFXmX6_Nao,18144
 brkraw/apps/addon/io.py,sha256=bjgwl0T1tsL02aAJtScLw3fnh2PfOlmK5aGAQj6WF8Y,413
 brkraw/apps/hook/__init__.py,sha256=W3xf6VmPZkVtQMwnYIrl626fnlck6bO20St0C45tMNY,398
-brkraw/apps/hook/core.py,sha256=z6PpwHYYESJD8EO__qVsXZj31YqP5JSSmNHYVHZRCnk,20720
+brkraw/apps/hook/core.py,sha256=C_EF_Z5k1-owG46DtEzp7SL9Db3mnbIzB1gKZBM6Owo,21327
 brkraw/apps/loader/__init__.py,sha256=ih3YNHm2JQpR_5bWNpKwzVImXg4rl6eK8C_40texwr0,101
-brkraw/apps/loader/core.py,sha256=NfwxZyp85CBtjSzT72zU91Hg1MafkVvEnHhvradD6OA,22460
+brkraw/apps/loader/core.py,sha256=FKc-ux2_zo413jNA3ENoB_xWq8eX05a-cy1Idrguw7o,22196
 brkraw/apps/loader/formatter.py,sha256=oiGO942bZMZODxI8kgYE0gdX4FLjwaZTquvZN3yGeeU,9315
 brkraw/apps/loader/helper.py,sha256=dujao_UH8C6aeZQ-GCTwCleoa-ZkrIDYSKlgwSN6gwA,34574
-brkraw/apps/loader/types.py,sha256=0w82elJXF0wYPZQ3eKiPTAR1vdearWnUtNH6CNzyYNo,6226
+brkraw/apps/loader/types.py,sha256=MzQOQCZ0HLfBqUMvXaSEi53OdI9u-ZCozAcjdod2apY,6248
 brkraw/apps/loader/info/__init__.py,sha256=1tWVkBakwf3LZK-FwsMrt10fkkdz9cWw1j-Y4Dk6Lio,164
 brkraw/apps/loader/info/scan.py,sha256=omq7d00huVNY2ClMwkEclWWe2a8P3AZV42Xy0vG7YUk,2837
-brkraw/apps/loader/info/scan.yaml,sha256=tYyGRg4t_rf6jGZAT8F0_dUA9MlQeZ5zeOuTNQ2wQM8,1728
+brkraw/apps/loader/info/scan.yaml,sha256=0LzH5AawmIiQ_3PTkwn9qeEp3xqndMDKBXnOWzXAypo,1787
 brkraw/apps/loader/info/study.py,sha256=0_5gUlDOd5xsmXaYF9pyhwUKsq3-oCZ5SMvH6RqlPp4,2743
-brkraw/apps/loader/info/study.yaml,sha256=M_wAy-B-4SErZ610KSNiqUW8aotorXkomymMYFdlyJw,3713
+brkraw/apps/loader/info/study.yaml,sha256=2-O24oQtQzgenjC1lPIdCd5FgEv2j4q4qXPitsdf424,3711
 brkraw/apps/loader/info/transform.py,sha256=gXYtIlbAwaLZX1K7jRFgFAJRG9D-zqlLQ-89BJOhuxM,2558
 brkraw/cli/__init__.py,sha256=Z97T007Iut9FMPWTRa7MDcUhd9uQhhQ0qmRJ1H4owlw,89
 brkraw/cli/hook_args.py,sha256=B2CKdSmZqSoQaBW4SMtjCXLLheDt-NJ1VwgvGp4Mtzw,2625
 brkraw/cli/main.py,sha256=OC6BBvSMTZdXz6tdArt163qfvDsldkAXLZ8osBFShFs,4086
-brkraw/cli/utils.py,sha256=dyEFydR7SsKUhSyHESqZqzAVu1zc2iLSA7GwG_OQ6FM,1348
+brkraw/cli/utils.py,sha256=wEN2Paehe11-Ho-jwg_KRewKhEnDM7sRMvKWCHgAGU4,1564
 brkraw/cli/commands/__init__.py,sha256=PHh4jqD7i0aL8W8hXThczKcT4xsNZiXanBxOH5IOW5I,36
 brkraw/cli/commands/addon.py,sha256=ctPJ6h_SPFovT1EY6iY-Fyrhfcu0Lo3oCvDz52YsKNM,11179
 brkraw/cli/commands/cache.py,sha256=wyGjM7WjIW8jcwRoEoUpSdlnzCLUTcozpan2KEG8i5Q,2254
 brkraw/cli/commands/config.py,sha256=qWj4yPNDeikLmONZw8-g1C098t-2oGCExJtam-fb6Pk,6480
-brkraw/cli/commands/convert.py,sha256=wWm4inT3Jb5DFNXuB0RZt96DqJ-FSPRvCj7FoVGGqic,31880
-brkraw/cli/commands/hook.py,sha256=esRVd-t_SGJDKvdfNlPd0belOqZNjLGMVXE1l0N1tbc,11889
-brkraw/cli/commands/info.py,sha256=Cog04r1oJYhIGQrfxH9JhLQLt6rwFSfJMuVN38MIDPI,2251
+brkraw/cli/commands/convert.py,sha256=uB0Qp1SViXdJKJvGE60cFDIRV5s4EJB2Gr472nRPP-E,32092
+brkraw/cli/commands/hook.py,sha256=1EYQHl-P_dPHpPBY5XUKgajI9lc9oi6fsIBj13xvzEQ,12431
+brkraw/cli/commands/info.py,sha256=9V6Qlp57Pg4qEaSjW8w6EpW8Orm-5lzdRm5po8qsglQ,2239
 brkraw/cli/commands/init.py,sha256=4LC0XHmZsGGozoNq2vlGBF6Y1MtbK77Ub7wVbwo9ACc,6957
 brkraw/cli/commands/params.py,sha256=LtYgXdffJ4PuXb5FMcRQhvHpRlFN28MIkpd0UMNx9-Y,3159
-brkraw/cli/commands/prune.py,sha256=RFH0GCkiu9EJNDUHg9lwH2DNBa9A-Yx9sIcUqITRrkg,8791
+brkraw/cli/commands/prune.py,sha256=z1RDbw8wECtJrvuP1f9LOooI822a5dz1yCLqWz_rMww,8805
 brkraw/cli/commands/session.py,sha256=t77PyNZpQoXxpszpqiKsOsKfLg9woXBJA_yinVhuEVk,12299
 brkraw/core/__init__.py,sha256=9UPOF5mtjZdGgjQ6-JJJs-eg8CGl4BuV7flGDWKgCBg,218
 brkraw/core/cache.py,sha256=oF6MOIrywGUrU9l8OweoBVww5ZSqv9BtALjNaPnr59Q,2324
@@ -56,12 +56,12 @@ brkraw/default/rules/00_default.yaml,sha256=a4PZOR0oam0ziZqLsvaQZqwoDu-uXbPVdxJc
 brkraw/default/specs/metadata_dicom.yaml,sha256=grrwGOBIIEUJPTs6vktWydnEsvBTjbgwez0190Q8ma0,4295
 brkraw/default/specs/metadata_transforms.py,sha256=illM4MKwwz-6PPKLrIno5lba1f5zKC8y09PAR5gCH1o,2383
 brkraw/resolver/__init__.py,sha256=2vz8b135CA4aebHUHSc2Hgtc3Ko2-qbdAxfTnUtTeGk,84
-brkraw/resolver/affine.py,sha256=s7vm30C5fkmOMTuY-Bc5lZeE3Wy4pbHydL1V4gzkDB4,19501
+brkraw/resolver/affine.py,sha256=wpCEnOjauYEecWlmSZqY-_ebeZTcN1zsmdKYZPO2Owc,21034
 brkraw/resolver/datatype.py,sha256=a1bqsGibtnRGGiPKAGbkXj1-Tyjmk52pUPgXM8F2px8,2522
 brkraw/resolver/fid.py,sha256=SXglNSD6hFK7pAoHrUvuNbCYPgIAvbRdh6PACp7Oz7g,2847
 brkraw/resolver/helpers.py,sha256=BpL-zpbtGae6n-XQOmD5qP7KrD5HFnElzAD3bcBq0J4,1029
 brkraw/resolver/image.py,sha256=9G3PRgQnSiU2dS23WxhoV_L-ekWnuY9z9pVwzTOF7ag,10716
-brkraw/resolver/nifti.py,sha256=S4Z1NZdJp0LbipyUndEUoJqQzAjGfoizhGQC9byQG38,12617
+brkraw/resolver/nifti.py,sha256=h4hOWebgMRl0LpNUEPbFybJ3tN9oj7J4zw2wKtABWLo,12635
 brkraw/resolver/shape.py,sha256=r2sQpgKGMN0nmBPj9_LTt7d3ls-y4R8n1HIMDvpNdfk,8110
 brkraw/schema/__init__.py,sha256=eEYYkxX5Hz9woXVOBJ2H2_CQoEih0vH6nRt3sH2Z8v8,49
 brkraw/schema/context_map.yaml,sha256=OUtoa7NgQZ7ytUe8zuNiJ5ratt1p0DRrrfDAP5Kthqs,1798
@@ -85,8 +85,8 @@ brkraw/specs/remapper/validator.py,sha256=R-Pib4MCgUVYAvAAoFR04bF-j7TDaePj-jGaxO
 brkraw/specs/rules/__init__.py,sha256=oF1ury9vxTYMlTgz9Yo9um8jRAzaJeTMwjAcDLV-KOE,214
 brkraw/specs/rules/logic.py,sha256=PbcvkyTjGKJn5CLg_V5QgnWNKirAqRrV3e1YVRx8FyQ,9092
 brkraw/specs/rules/validator.py,sha256=AHS-r-E0HGHxwhhU48nCyS6LQvllQCgXLS_NDXBm3-k,3508
-brkraw-0.5.5.dist-info/METADATA,sha256=stg8aCKjoMzzB0VCtjN7F1GunvD73ybWshFCLwkXcqY,3058
-brkraw-0.5.5.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-brkraw-0.5.5.dist-info/entry_points.txt,sha256=fdCNXyFoqRsPYXXizC_LS44B9Myjr1dH2tewvtcIN-E,493
-brkraw-0.5.5.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-brkraw-0.5.5.dist-info/RECORD,,
+brkraw-0.5.7.dist-info/METADATA,sha256=_ZnDJuPxq8GeszcdNfWXfZGV1njLBdI_muXN9-DoJmc,3058
+brkraw-0.5.7.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+brkraw-0.5.7.dist-info/entry_points.txt,sha256=fdCNXyFoqRsPYXXizC_LS44B9Myjr1dH2tewvtcIN-E,493
+brkraw-0.5.7.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+brkraw-0.5.7.dist-info/RECORD,,