brkraw 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

brkraw/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-__version__ = '0.5.1'
+__version__ = '0.5.3'
 from .apps.loader import BrukerLoader
 
 

brkraw/apps/loader/core.py

@@ -163,6 +163,7 @@ class BrukerLoader:
             scan.convert = MethodType(_convert, scan)
             scan._converter_hook = None
             scan._converter_hook_name = None
+            scan.converter_func = None
             if rules:
                 try:
                     hook_name = select_rule_use(
@@ -259,9 +260,8 @@ class BrukerLoader:
             partial(_get_affine, decimals=self._affine_decimals),
             scan,
         )
-        scan.get_nifti1image = MethodType(_get_nifti1image, scan)
-        scan.convert = MethodType(_convert, scan)
         scan._converter_hook = None
+        scan.converter_func = None
 
     def get_scan(self, scan_id: int) -> "ScanLoader":
         """Return scan by id.
@@ -349,7 +349,6 @@ class BrukerLoader:
                         override_header: Optional[Nifti1HeaderContents] = None,
                         override_subject_type: Optional[SubjectType] = None,
                         override_subject_pose: Optional[SubjectPose] = None,
-                        flip_x: bool = False, 
                         flatten_fg: bool = False,
                         xyz_units: XYZUNIT = 'mm', 
                         t_units: TUNIT = 'sec'):
@@ -362,7 +361,6 @@ class BrukerLoader:
             override_header: Optional header values to apply.
             override_subject_type: Subject type override for subject view.
             override_subject_pose: Subject pose override for subject view.
-            flip_x: If True, set NIfTI header x-flip flag.
             xyz_units: Spatial units for NIfTI header.
             t_units: Temporal units for NIfTI header.
 
@@ -372,12 +370,10 @@ class BrukerLoader:
         scan = self.get_scan(scan_id)
         return scan.convert(
             reco_id,
-            format="nifti",
             space=space,
             override_header=override_header,
             override_subject_type=override_subject_type,
             override_subject_pose=override_subject_pose,
-            flip_x=flip_x,
             flatten_fg=flatten_fg,
             xyz_units=xyz_units,
             t_units=t_units,
@@ -388,27 +384,23 @@ class BrukerLoader:
         scan_id: int,
         reco_id: Optional[int] = None,
         *,
-        format: Literal["nifti", "nifti1"] = "nifti",
         space: AffineSpace = 'subject_ras',
         override_header: Optional[Nifti1HeaderContents] = None,
         override_subject_type: Optional[SubjectType] = None,
         override_subject_pose: Optional[SubjectPose] = None,
-        flip_x: bool = False,
         flatten_fg: bool = False,
         xyz_units: XYZUNIT = "mm",
         t_units: TUNIT = "sec",
         hook_args_by_name: Optional[Mapping[str, Mapping[str, Any]]] = None,
     ):
-        """Convert a scan/reco to the requested output format."""
+        """Convert a scan/reco to output object(s) supporting to_filename()."""
         scan = self.get_scan(scan_id)
         return scan.convert(
             reco_id,
-            format=format,
             space=space,
             override_header=override_header,
             override_subject_type=override_subject_type,
             override_subject_pose=override_subject_pose,
-            flip_x=flip_x,
             flatten_fg=flatten_fg,
             xyz_units=xyz_units,
             t_units=t_units,

brkraw/apps/loader/helper.py

@@ -21,7 +21,7 @@ from ...core.parameters import Parameters
 from ...specs.remapper import load_spec, map_parameters, load_context_map, apply_context_map
 from ...specs.rules import load_rules, select_rule_use
 from ...dataclasses import Reco, Scan, Study
-from .types import ScanLoader
+from .types import ScanLoader, ToFilename, ConvertType, GetDataobjType, GetAffineType
 from ...specs import hook as converter_core
 from ...resolver import affine as affine_resolver
 from ...resolver import image as image_resolver
@@ -472,6 +472,54 @@ def _apply_affine_post_transform(affines: AffineReturn, *, kwargs: Mapping[str,
 
 
 def get_nifti1image(
+    self: Union["Scan", "ScanLoader"],
+    reco_id: int,
+    dataobjs: Tuple[np.ndarray, ...],
+    affines: Tuple[np.ndarray, ...],
+    *,
+    xyz_units: XYZUNIT = "mm",
+    t_units: TUNIT = "sec",
+    override_header: Optional[Nifti1HeaderContents] = None,
+) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
+    """Return NIfTI image(s) for a reco.
+
+    Args:
+        self: Scan or ScanLoader instance.
+        reco_id: Reco identifier to read (defaults to the first available).
+        xyz_units: Spatial units for NIfTI header.
+        t_units: Temporal units for NIfTI header.
+        override_header: Optional header values to apply.
+
+    Returns:
+        Output object(s) supporting to_filename(). Returns None when required
+        metadata is unavailable.
+    """
+    self = cast(ScanLoader, self)
+    
+    image_info = self.image_info.get(reco_id)
+    if dataobjs is None or affines is None or image_info is None:
+        return None
+
+    niiobjs = []
+    for i, dataobj in enumerate(dataobjs):
+        affine = affines[i]
+        niiobj = Nifti1Image(dataobj, affine)
+        nifti1header_contents = nifti_resolver.resolve(
+            image_info, xyz_units=xyz_units, t_units=t_units
+        )
+        if override_header:
+            for key, value in override_header.items():
+                if value is not None:
+                    nifti1header_contents[key] = value
+        niiobj = nifti_resolver.update(niiobj, nifti1header_contents)
+        niiobjs.append(niiobj)
+
+    if len(niiobjs) == 1:
+        return niiobjs[0]
+    return tuple(niiobjs)
+
+
+def convert(
     self: Union["Scan", "ScanLoader"],
     reco_id: Optional[int] = None,
     *,
@@ -479,30 +527,30 @@ def get_nifti1image(
     override_header: Optional[Nifti1HeaderContents] = None,
     override_subject_type: Optional[SubjectType] = None,
     override_subject_pose: Optional[SubjectPose] = None,
-    flip_x: bool = False,
     flatten_fg: bool = False,
     xyz_units: XYZUNIT = "mm",
     t_units: TUNIT = "sec",
     hook_args_by_name: Optional[Mapping[str, Mapping[str, Any]]] = None,
-) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
-    """Return NIfTI image(s) for a reco.
-
+    **kwargs: Any,
+) -> Optional[Union["ToFilename", Tuple["ToFilename", ...]]]:
+    """Convert a reco to output object(s).
+    
     Args:
-        self: Scan or ScanLoader instance.
-        reco_id: Reco identifier to read (defaults to the first available).
         space: Output affine space ("raw", "scanner", "subject_ras").
         override_header: Optional header values to apply.
         override_subject_type: Subject type override for subject-view wrapping.
         override_subject_pose: Subject pose override for subject-view wrapping.
-        flip_x: If True, set NIfTI header x-flip flag.
+        flatten_fg: If True, flatten foreground dimensions.
+        xyz_units: Spatial units for NIfTI header.
+        t_units: Temporal units for NIfTI header.
+        hook_args_by_name: Optional hook args mapping (split per helper signature).
+        flatten_fg: If True, flatten foreground dimensions.
         xyz_units: Spatial units for NIfTI header.
         t_units: Temporal units for NIfTI header.
-
     Returns:
         Single NIfTI image when one slice pack exists; otherwise a tuple of
         images. Returns None when required metadata is unavailable.
     """
-
     if not all(
         hasattr(self, attr) for attr in ["image_info", "affine_info", "get_dataobj", "get_affine"]
     ):
@@ -512,14 +560,57 @@ def get_nifti1image(
     resolved_reco_id = _resolve_reco_id(self, reco_id)
     if resolved_reco_id is None:
         return None
+
+    hook_name = getattr(self, "_converter_hook_name", None)
+    if isinstance(hook_name, str) and hook_name:
+        logger.debug(
+            "Convert starting for scan %s reco %s with hook %s",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+            hook_name,
+        )
+    else:
+        logger.debug(
+            "Convert starting for scan %s reco %s (no hook)",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+        )
+    
     hook_kwargs = _resolve_hook_kwargs(self, hook_args_by_name)
     data_kwargs = _filter_hook_kwargs(self.get_dataobj, hook_kwargs)
+    convert_kwargs = {
+        key: value
+        for key, value in hook_kwargs.items()
+        if key not in data_kwargs
+    }
     if data_kwargs:
+        logger.debug(
+            "Calling get_dataobj for scan %s reco %s with args %s",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+            data_kwargs,
+        )
         dataobjs = self.get_dataobj(resolved_reco_id, **data_kwargs)
     else:
+        logger.debug(
+            "Calling get_dataobj for scan %s reco %s (no args)",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+        )
         dataobjs = self.get_dataobj(resolved_reco_id)
     affine_kwargs = _filter_hook_kwargs(self.get_affine, hook_kwargs)
+    convert_kwargs = {
+        key: value
+        for key, value in convert_kwargs.items()
+        if key not in affine_kwargs
+    }
     if affine_kwargs:
+        logger.debug(
+            "Calling get_affine for scan %s reco %s with args %s",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+            affine_kwargs,
+        )
         affines = self.get_affine(
             resolved_reco_id,
             space=space,
@@ -528,77 +619,64 @@ def get_nifti1image(
             **affine_kwargs,
         )
     else:
+        logger.debug(
+            "Calling get_affine for scan %s reco %s (no args)",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+        )
         affines = self.get_affine(
             resolved_reco_id,
             space=space,
             override_subject_type=override_subject_type,
             override_subject_pose=override_subject_pose,
         )
-    image_info = self.image_info.get(resolved_reco_id)
-
-    if dataobjs is None or affines is None or image_info is None:
+    
+    if dataobjs is None or affines is None:
         return None
-
-    if not isinstance(dataobjs, tuple) and not isinstance(affines, tuple):
+    
+    if not isinstance(dataobjs, tuple):
         dataobjs = (dataobjs,)
+    if not isinstance(affines, tuple):
         affines = (affines,)
-
-    niiobjs = []
+    
+    dataobjs = list(dataobjs)
     for i, dataobj in enumerate(dataobjs):
         if flatten_fg and dataobj.ndim > 4:
             spatial_shape = dataobj.shape[:3]
             flattened = int(np.prod(dataobj.shape[3:]))
-            dataobj = dataobj.reshape((*spatial_shape, flattened), order="A")
-        affine = affines[i]
-        niiobj = Nifti1Image(dataobj, affine)
-        nifti1header_contents = nifti_resolver.resolve(
-            image_info, flip_x=flip_x, xyz_units=xyz_units, t_units=t_units
+            dataobjs[i] = dataobj.reshape((*spatial_shape, flattened), order="A")
+    dataobjs = tuple(dataobjs)
+     
+    converter_func = getattr(self, "converter_func", None)
+    if isinstance(converter_func, ConvertType):
+        hook_call_kwargs = _filter_hook_kwargs(converter_func, convert_kwargs)
+        logger.debug(
+            "Calling converter hook for scan %s reco %s with args %s",
+            getattr(self, "scan_id", "?"),
+            resolved_reco_id,
+            hook_call_kwargs,
+        )
+        return converter_func(
+            dataobj=dataobjs,
+            affine=affines,
+            **hook_call_kwargs,
         )
-        if override_header:
-            for key, value in override_header.items():
-                if value is not None:
-                    nifti1header_contents[key] = value
-        niiobj = nifti_resolver.update(niiobj, nifti1header_contents)
-        niiobjs.append(niiobj)
-
-    if len(niiobjs) == 1:
-        return niiobjs[0]
-    return tuple(niiobjs)
-
 
-def convert(
-    self: Union["Scan", "ScanLoader"],
-    reco_id: Optional[int] = None,
-    *,
-    format: Literal["nifti", "nifti1"] = "nifti",
-    space: AffineSpace = "subject_ras",
-    override_header: Optional[Nifti1HeaderContents] = None,
-    override_subject_type: Optional[SubjectType] = None,
-    override_subject_pose: Optional[SubjectPose] = None,
-    flip_x: bool = False,
-    flatten_fg: bool = False,
-    xyz_units: XYZUNIT = "mm",
-    t_units: TUNIT = "sec",
-    hook_args_by_name: Optional[Mapping[str, Mapping[str, Any]]] = None,
-) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
-    """Convert a reco to a selected output format."""
-    if format not in {"nifti", "nifti1"}:
-        raise ValueError(f"Unsupported format: {format}")
+    nifti1image_kwargs = {
+        "xyz_units": xyz_units,
+        "t_units": t_units,
+        "override_header": override_header,
+        **kwargs,
+    }
+    nifti1image_kwargs = _filter_hook_kwargs(get_nifti1image, nifti1image_kwargs)
     return get_nifti1image(
         self,
-        reco_id,
-        space=space,
-        override_header=override_header,
-        override_subject_type=override_subject_type,
-        override_subject_pose=override_subject_pose,
-        flip_x=flip_x,
-        flatten_fg=flatten_fg,
-        xyz_units=xyz_units,
-        t_units=t_units,
-        hook_args_by_name=hook_args_by_name,
+        reco_id=resolved_reco_id,
+        dataobjs=dataobjs,
+        affines=affines,
+        **nifti1image_kwargs,
     )
 
-
 def _resolve_hook_kwargs(
     scan: Union["Scan", "ScanLoader"],
     hook_args_by_name: Optional[Mapping[str, Mapping[str, Any]]],
@@ -608,6 +686,12 @@ def _resolve_hook_kwargs(
     hook_name = getattr(scan, "_converter_hook_name", None)
     if not isinstance(hook_name, str) or not hook_name:
         return {}
+    logger.debug(
+        "Resolving hook args for scan %s hook %s (available: %s)",
+        getattr(scan, "scan_id", "?"),
+        hook_name,
+        sorted(hook_args_by_name.keys()),
+    )
     values = hook_args_by_name.get(hook_name)
     if values is None:
         seen: set[str] = set()
@@ -643,7 +727,12 @@ def _resolve_hook_kwargs(
                 )
                 values = candidate_values
                 break
-    return dict(values) if isinstance(values, Mapping) else {}
+    resolved = dict(values) if isinstance(values, Mapping) else {}
+    if resolved:
+        logger.debug("Resolved hook args for %s: %s", hook_name, resolved)
+    else:
+        logger.debug("No hook args resolved for %s.", hook_name)
+    return resolved
 
 
 def _filter_hook_kwargs(func: Any, hook_kwargs: Mapping[str, Any]) -> Dict[str, Any]:
@@ -785,6 +874,17 @@ def apply_converter_hook(
     """Override scan conversion helpers using a converter hook."""
     converter_core.validate_hook(converter_hook)
     plugin = dict(converter_hook)
+    logger.debug(
+        "Binding converter hook for scan %s: %s",
+        getattr(scan, "scan_id", "?"),
+        sorted(plugin.keys()),
+    )
+    if "get_dataobj" in plugin and not isinstance(plugin["get_dataobj"], GetDataobjType):
+        raise TypeError("Converter hook 'get_dataobj' must match GetDataobjType.")
+    if "get_affine" in plugin and not isinstance(plugin["get_affine"], GetAffineType):
+        raise TypeError("Converter hook 'get_affine' must match GetAffineType.")
+    if "convert" in plugin and not isinstance(plugin["convert"], ConvertType):
+        raise TypeError("Converter hook 'convert' must match ConvertType.")
     scan._converter_hook = plugin
     if "get_dataobj" in plugin:
         scan.get_dataobj = MethodType(plugin["get_dataobj"], scan)
@@ -794,4 +894,11 @@ def apply_converter_hook(
             get_affine = partial(get_affine, decimals=affine_decimals)
         scan.get_affine = MethodType(get_affine, scan)
     if "convert" in plugin:
-        scan.convert = MethodType(plugin["convert"], scan)
+        scan.converter_func = MethodType(plugin["convert"], scan)
+    else:
+        scan.converter_func = None
+    logger.debug(
+        "Converter hook bound for scan %s (hook=%s)",
+        getattr(scan, "scan_id", "?"),
+        getattr(scan, "_converter_hook_name", None),
+    )

brkraw/apps/loader/types.py

@@ -5,7 +5,7 @@ Last updated: 2025-12-30
 
 from __future__ import annotations
 
-from typing import Any, Union, Tuple, Dict, Optional, Protocol, Literal, Mapping, Callable, List, TYPE_CHECKING
+from typing import Any, Union, Tuple, Dict, Optional, Protocol, Literal, Mapping, Callable, List, TYPE_CHECKING, runtime_checkable
 if TYPE_CHECKING:
     from typing_extensions import ParamSpec, TypeAlias
 else:
@@ -35,6 +35,7 @@ AffineSpace = Literal["raw", "scanner", "subject_ras"]
 P = ParamSpec("P")
 
 
+@runtime_checkable
 class GetDataobjType(Protocol[P]):
     """Callable signature for get_dataobj overrides."""
     def __call__(
@@ -47,6 +48,7 @@ class GetDataobjType(Protocol[P]):
         ...
 
 
+@runtime_checkable
 class GetAffineType(Protocol):
     """Callable signature for get_affine overrides."""
     def __call__(
@@ -63,44 +65,21 @@ class GetAffineType(Protocol):
         ...
 
 
-class GetNifti1ImageType(Protocol):
-    """Callable signature for get_nifti1image overrides."""
-    def __call__(
-        self,
-        scan: "Scan",
-        reco_id: Optional[int] = None,
-        *,
-        override_header: Optional[Union[dict, "Nifti1HeaderContents"]],
-        space: AffineSpace,
-        override_subject_type: Optional[SubjectType],
-        override_subject_pose: Optional[SubjectPose],
-        flip_x: bool,
-        flatten_fg: bool,
-        xyz_units: XYZUNIT,
-        t_units: TUNIT,
-        **kwargs: Any,
-    ) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
-        ...
-
-
+@runtime_checkable
 class ConvertType(Protocol):
     """Callable signature for convert overrides."""
     def __call__(
         self,
         scan: "Scan",
-        reco_id: Optional[int] = None,
-        *,
-        format: Union[Literal["nifti", "nifti1"], str],
-        override_header: Optional[Union[dict, "Nifti1HeaderContents"]],
-        space: AffineSpace,
-        override_subject_type: Optional[SubjectType],
-        override_subject_pose: Optional[SubjectPose],
-        flip_x: bool,
-        flatten_fg: bool,
-        xyz_units: XYZUNIT,
-        t_units: TUNIT,
+        dataobj: Union[Tuple["np.ndarray", ...], "np.ndarray"],
+        affine: Union[Tuple["np.ndarray", ...], "np.ndarray"],
         **kwargs: Any,
-    ) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
+    ) -> Optional[Union["ToFilename", Tuple["ToFilename", ...]]]:
+        ...
+
+class ToFilename(Protocol):
+    """Result object that can be written to disk."""
+    def to_filename(self, filename: Union[str, "Path"], *args: Any, **kwargs: Any) -> Any:
         ...
 
 
@@ -126,9 +105,11 @@ class ScanLoader(Scan, BaseLoader):
 
     image_info: Dict[int, Optional["ResolvedImage"]]
     affine_info: Dict[int, Optional["ResolvedAffine"]]
+    converter_func: Optional[ConvertType]
     _converter_hook: Optional[ConverterHook]
     _converter_hook_name: Optional[str]
-
+    
+    
     def get_fid(self, 
                 buffer_start: Optional[int], 
                 buffer_size: Optional[int], 
@@ -155,15 +136,12 @@ class ScanLoader(Scan, BaseLoader):
         ...
 
     def get_nifti1image(
-            self, 
-            reco_id: Optional[int] = None, 
+            self,
+            reco_id: int, 
+            dataobjs: Tuple["np.ndarray", ...],
+            affines: Tuple["np.ndarray", ...],
             *, 
             override_header: Optional[Union[dict, "Nifti1HeaderContents"]],
-            space: AffineSpace = "subject_ras",
-            override_subject_type: Optional[SubjectType],
-            override_subject_pose: Optional[SubjectPose],
-            flip_x: bool, 
-            flatten_fg: bool,
             xyz_units: XYZUNIT, 
             t_units: TUNIT
             ) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
@@ -173,17 +151,16 @@ class ScanLoader(Scan, BaseLoader):
             self,
             reco_id: Optional[int] = None,
             *,
-            format: Literal["nifti", "nifti1"],
-            override_header: Optional[Union[dict, "Nifti1HeaderContents"]],
             space: AffineSpace = "subject_ras",
+            override_header: Optional[Union[dict, "Nifti1HeaderContents"]],
             override_subject_type: Optional[SubjectType],
             override_subject_pose: Optional[SubjectPose],
-            flip_x: bool,
             flatten_fg: bool,
             xyz_units: XYZUNIT,
             t_units: TUNIT,
             hook_args_by_name: Optional[Mapping[str, Mapping[str, Any]]] = None,
-            ) -> Optional[Union[Tuple["Nifti1Image", ...], "Nifti1Image"]]:
+            **kwargs: Any,
+            ) -> Optional[Union["ToFilename", Tuple["ToFilename", ...]]]:
         ...
 
     def get_metadata(
@@ -201,15 +178,15 @@ class RecoLoader(Reco, BaseLoader):
     ...
 
 
-ConverterHook: TypeAlias = Mapping[str, Union[GetDataobjType[Any], GetAffineType, GetNifti1ImageType, ConvertType]]
+ConverterHook: TypeAlias = Mapping[str, Union[GetDataobjType[Any], GetAffineType, ConvertType]]
 """Mapping of converter hook keys to override callables."""
 
 
 __all__ = [
     'GetDataobjType',
     'GetAffineType',
-    'GetNifti1ImageType',
     'ConvertType',
+    'ToFilename',
     'ConverterHook',
     'StudyLoader',
     'ScanLoader',

brkraw/cli/commands/convert.py

@@ -13,7 +13,7 @@ import os
 import re
 import sys
 from pathlib import Path
-from typing import Any, Mapping, Optional, Dict, List, Tuple, Literal, cast, get_args
+from typing import Any, Mapping, Optional, Dict, List, Tuple, cast, get_args
 
 import numpy as np
 from brkraw.cli.utils import load
@@ -84,8 +84,6 @@ def cmd_convert(args: argparse.Namespace) -> int:
     if args.no_convert and not args.sidecar:
         logger.error("--no-convert requires --sidecar.")
         return 2
-    if not args.flip_x:
-        args.flip_x = _env_flag("BRKRAW_CONVERT_FLIP_X")
     if not args.flatten_fg:
         args.flatten_fg = _env_flag("BRKRAW_CONVERT_FLATTEN_FG")
     if args.space is None:
@@ -119,7 +117,6 @@ def cmd_convert(args: argparse.Namespace) -> int:
     if args.space is None:
         args.space = "subject_ras"
     for attr, env_key in (
-        ("format", "BRKRAW_CONVERT_FORMAT"),
         ("header", "BRKRAW_CONVERT_HEADER"),
         ("context_map", "BRKRAW_CONVERT_CONTEXT_MAP"),
     ):
@@ -139,13 +136,6 @@ def cmd_convert(args: argparse.Namespace) -> int:
             logger.error("Cannot use --prefix when --output is a file path.")
             return 2
 
-    args.format = _coerce_choice(
-        "BRKRAW_CONVERT_FORMAT",
-        args.format or "nifti",
-        ("nifti", "nifti1"),
-        default="nifti",
-    )
-
     try:
         render_layout_supports_counter = "counter" in inspect.signature(layout_core.render_layout).parameters
     except (TypeError, ValueError):
@@ -265,12 +255,10 @@ def cmd_convert(args: argparse.Namespace) -> int:
                 nii = loader.convert(
                     scan_id,
                     reco_id=reco_id,
-                    format=cast(Literal["nifti", "nifti1"], args.format),
                     space=cast(AffineSpace, args.space),
                     override_header=cast(Nifti1HeaderContents, override_header) if override_header else None,
                     override_subject_type=cast(Optional[SubjectType], args.override_subject_type),
                     override_subject_pose=cast(Optional[SubjectPose], args.override_subject_pose),
-                    flip_x=args.flip_x,
                     flatten_fg=args.flatten_fg,
                     xyz_units=cast(XYZUNIT, args.xyz_units),
                     t_units=cast(TUNIT, args.t_units),
@@ -686,7 +674,10 @@ def _parse_hook_args(values: List[str]) -> Dict[str, Dict[str, Any]]:
         key = key.strip()
         if not hook_name or not key:
             raise ValueError("Hook args must include hook name and key.")
-        parsed.setdefault(hook_name, {})[key] = _coerce_scalar(value.strip())
+        coerced_value = _coerce_scalar(value.strip())
+        logger.debug("Parsed hook arg %s:%s=%s", hook_name, key, coerced_value)
+        parsed.setdefault(hook_name, {})[key] = coerced_value
+    logger.debug("Parsed hook args: %s", parsed)
     return parsed
 
 
@@ -781,11 +772,6 @@ def _add_convert_args(
             type=int,
             help="Reco id to convert (defaults to all recos when omitted).",
         )
-    parser.add_argument(
-        "--flip-x",
-        action="store_true",
-        help="Flip x-axis in NIfTI header.",
-    )
     parser.add_argument(
         "--xyz-units",
         choices=list(get_args(XYZUNIT)),
@@ -854,11 +840,6 @@ def _add_convert_args(
         choices=list(get_args(SubjectPose)),
         help="Override subject pose for subject-view affines (space=subject_ras).",
     )
-    parser.add_argument(
-        "--format",
-        choices=["nifti", "nifti1"],
-        help="Output format (default: nifti).",
-    )
     parser.add_argument(
         "--flatten-fg",
         action="store_true",

brkraw/cli/commands/hook.py

@@ -178,12 +178,10 @@ _PRESET_IGNORE_PARAMS = frozenset(
         "scan",
         "scan_id",
         "reco_id",
-        "format",
         "space",
         "override_header",
         "override_subject_type",
         "override_subject_pose",
-        "flip_x",
         "xyz_units",
         "t_units",
         "decimals",

brkraw/cli/commands/session.py

@@ -98,14 +98,12 @@ def cmd_unset(args: argparse.Namespace) -> int:
         "BRKRAW_CONVERT_CONTEXT_MAP",
         "BRKRAW_CONVERT_SPACE",
         "BRKRAW_CONVERT_COMPRESS",
-        "BRKRAW_CONVERT_FLIP_X",
         "BRKRAW_CONVERT_FLATTEN_FG",
         "BRKRAW_CONVERT_OVERRIDE_SUBJECT_TYPE",
         "BRKRAW_CONVERT_OVERRIDE_SUBJECT_POSE",
         "BRKRAW_CONVERT_XYZ_UNITS",
         "BRKRAW_CONVERT_T_UNITS",
         "BRKRAW_CONVERT_HEADER",
-        "BRKRAW_CONVERT_FORMAT",
     ]
     targets: List[str] = []
     if args.path:
@@ -153,14 +151,12 @@ def cmd_env(_: argparse.Namespace) -> int:
     convert_context_map = os.environ.get("BRKRAW_CONVERT_CONTEXT_MAP")
     convert_compress = os.environ.get("BRKRAW_CONVERT_COMPRESS")
     convert_space = os.environ.get("BRKRAW_CONVERT_SPACE")
-    convert_flip_x = os.environ.get("BRKRAW_CONVERT_FLIP_X")
     convert_flatten_fg = os.environ.get("BRKRAW_CONVERT_FLATTEN_FG")
     convert_subject_type = os.environ.get("BRKRAW_CONVERT_OVERRIDE_SUBJECT_TYPE")
     convert_subject_pose = os.environ.get("BRKRAW_CONVERT_OVERRIDE_SUBJECT_POSE")
     convert_xyz_units = os.environ.get("BRKRAW_CONVERT_XYZ_UNITS")
     convert_t_units = os.environ.get("BRKRAW_CONVERT_T_UNITS")
     convert_header = os.environ.get("BRKRAW_CONVERT_HEADER")
-    convert_format = os.environ.get("BRKRAW_CONVERT_FORMAT")
     if (
         path is None
         and scan_id is None
@@ -175,14 +171,12 @@ def cmd_env(_: argparse.Namespace) -> int:
         and convert_context_map is None
         and convert_compress is None
         and convert_space is None
-        and convert_flip_x is None
         and convert_flatten_fg is None
         and convert_subject_type is None
         and convert_subject_pose is None
         and convert_xyz_units is None
         and convert_t_units is None
         and convert_header is None
-        and convert_format is None
     ):
         print("(none)")
         return 0
@@ -212,8 +206,6 @@ def cmd_env(_: argparse.Namespace) -> int:
         print(f"BRKRAW_CONVERT_SPACE={convert_space}")
     if convert_compress is not None:
         print(f"BRKRAW_CONVERT_COMPRESS={convert_compress}")
-    if convert_flip_x is not None:
-        print(f"BRKRAW_CONVERT_FLIP_X={convert_flip_x}")
     if convert_flatten_fg is not None:
         print(f"BRKRAW_CONVERT_FLATTEN_FG={convert_flatten_fg}")
     if convert_subject_type is not None:
@@ -226,8 +218,6 @@ def cmd_env(_: argparse.Namespace) -> int:
         print(f"BRKRAW_CONVERT_T_UNITS={convert_t_units}")
     if convert_header is not None:
         print(f"BRKRAW_CONVERT_HEADER={convert_header}")
-    if convert_format is not None:
-        print(f"BRKRAW_CONVERT_FORMAT={convert_format}")
     return 0
 
 
@@ -311,7 +301,7 @@ def register(subparsers: argparse._SubParsersAction) -> None:  # type: ignore[na
         help=(
             "Set BRKRAW_CONVERT_<OPTION> as KEY=VALUE (repeatable). "
             "Keys: OUTPUT, PREFIX, SCAN_ID, RECO_ID, SIDECAR, CONTEXT_MAP, "
-            "COMPRESS, SPACE, FLIP_X, FLATTEN_FG, OVERRIDE_SUBJECT_TYPE, "
+            "COMPRESS, SPACE, FLATTEN_FG, OVERRIDE_SUBJECT_TYPE, "
             "OVERRIDE_SUBJECT_POSE, XYZ_UNITS, T_UNITS, HEADER, FORMAT."
         ),
     )

brkraw/resolver/nifti.py

@@ -32,7 +32,6 @@ DimInfo = Tuple[Optional[int], Optional[int], Optional[int]]
 logger = logging.getLogger("brkraw")
 
 class Nifti1HeaderContents(TypedDict, total=False):
-    flip_x: bool
     slice_code: int
     slope_inter: Tuple[float, float]
     time_step: Optional[float]
@@ -57,7 +56,6 @@ class Nifti1HeaderContents(TypedDict, total=False):
 _XYZ_UNITS = set(get_args(XYZUNIT))
 _T_UNITS = set(get_args(TUNIT))
 _HEADER_FIELDS = {
-    "flip_x",
     "slice_code",
     "slope_inter",
     "time_step",
@@ -159,9 +157,7 @@ def _coerce_header_contents(data: Mapping[str, Any]) -> Nifti1HeaderContents:
                 header[key] = None
                 continue
             raise ValueError(f"{key} cannot be null.")
-        if key == "flip_x":
-            header[key] = _coerce_bool(value, name=key)
-        elif key in {"slice_code", "qform_code", "sform_code", "slice_start", "slice_end", "intent_code"}:
+        if key in {"slice_code", "qform_code", "sform_code", "slice_start", "slice_end", "intent_code"}:
             header[key] = int(value)
         elif key in {"time_step", "slice_duration", "cal_min", "cal_max"}:
             header[key] = float(value)
@@ -247,9 +243,8 @@ def _set_dataobj(niiobj: "Nifti1Image", dataobj: np.ndarray) -> None:
 
 
 def resolve(
-    image_info: "ResolvedImage", 
-    flip_x: bool = False, 
-    xyz_units: "XYZUNIT" = 'mm', 
+    image_info: "ResolvedImage",
+    xyz_units: "XYZUNIT" = 'mm',
     t_units: "TUNIT" = 'sec'
 ) -> Nifti1HeaderContents:
     
@@ -273,7 +268,6 @@ def resolve(
     slope = image_info['slope']
     offset = image_info['offset']
     result: Nifti1HeaderContents = {
-        'flip_x': flip_x,
         'slice_code': slice_code,
         'slope_inter': (slope, offset),
         'time_step': time_step,
@@ -295,9 +289,7 @@ def update(
     for c, val in nifti1header_contents.items():
         if val is None or c in ('qform_code', 'sform_code'):
             continue
-        if c == 'flip_x':
-            niiobj.header.default_x_flip = bool(val)
-        elif c == "slice_code":
+        if c == "slice_code":
             if _coerce_int(val, name="slice_code") != 0:
                 niiobj.header['slice_code'] = _coerce_int(val, name="slice_code")
         elif c == "slope_inter":

brkraw/schema/niftiheader.yaml

@@ -4,8 +4,6 @@ title: "BrkRaw NIfTI Header Overrides"
 type: object
 additionalProperties: false
 properties:
-  flip_x:
-    type: boolean
   slice_code:
     type: integer
   slope_inter:

{brkraw-0.5.1.dist-info → brkraw-0.5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brkraw
-Version: 0.5.1
+Version: 0.5.3
 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>
@@ -31,6 +31,7 @@ Requires-Dist: mkdocs; extra == 'dev'
 Requires-Dist: mkdocs-material; extra == 'dev'
 Requires-Dist: pymdown-extensions; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: tomli; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: rich; extra == 'docs'
 Provides-Extra: minimal
@@ -48,7 +49,7 @@ Description-Content-Type: text/markdown
 
 A modular toolkit for Bruker MRI raw-data handling.
 
-BrkRaw (v0.5.1) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.3) converts raw data into standardized, neuroimaging-ready
 datasets, with extensible rules/specs and plugin hooks.
 
 - Documentation: [brkraw.github.io](https://brkraw.github.io/)
@@ -66,16 +67,14 @@ If you use BrkRaw in your research, please cite it.
 
 <!-- BEGIN: brkraw-bibtex -->
 ```biblatex
-@software{brkraw_2026,
-  author = {Lee, Sung-Ho and Devenyi, Gabriel A and Ban, Woomi and Shih, Yen-Yu Ian},
+@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},
-  year = {2026},
-  version = {0.5.0},
+  version = {0.5.2},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},
-  license = {GPL-3.0-only},
-  date = {2026-01-13}
+  license = {GPL-3.0-only}
 }
 ```
 <!-- END: brkraw-bibtex -->

{brkraw-0.5.1.dist-info → brkraw-0.5.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-brkraw/__init__.py,sha256=xRDzaw80M_f5rceXUn0qFpdFc04QizjLqQ4XnZjM1iw,210
+brkraw/__init__.py,sha256=p-zGQeH33UEQNKlOOYjQ9gSsfb2MzdTREjhA-sQbI4g,210
 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
@@ -8,10 +8,10 @@ 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/loader/__init__.py,sha256=ytG3wTI3mRHxkLkZ3GNYA6LJduplYgUinZBMuJJkeMQ,163
-brkraw/apps/loader/core.py,sha256=hyc7gk-Bl5g5_bMUdnSY99xjjY9YOt3P0o25QIo0zzE,23268
+brkraw/apps/loader/core.py,sha256=m2BGF4E8QqoW1wuVnPf09RjK4Q_mQNMJ0rUQCXibteE,22941
 brkraw/apps/loader/formatter.py,sha256=WWVCVKdZl6vdyKPCW6rLRmwKuF1cCTTNMPP0vmyBF6Y,9341
-brkraw/apps/loader/helper.py,sha256=Vf8nqgH3KBGIf74f52wcnB1rINEVViUM2O4W8FeGmNs,27879
-brkraw/apps/loader/types.py,sha256=F3EXtV5vEYlHvCBRwjlz3iaTaJiSe7CYC6IayP_bbug,6825
+brkraw/apps/loader/helper.py,sha256=n-8RHDB4TNV6V3RWbfe96iK-0ATzQ4yysiRVVZ4VRuw,31569
+brkraw/apps/loader/types.py,sha256=5ijIMSwvAg1ZoQb8zrAajKXygTwLXPb7evOE_fufL0U,6014
 brkraw/apps/loader/info/__init__.py,sha256=1tWVkBakwf3LZK-FwsMrt10fkkdz9cWw1j-Y4Dk6Lio,164
 brkraw/apps/loader/info/scan.py,sha256=_oLBG7YlwVUv1vWXBvCZbXQiMvC1ARKCRNTvrAkqO0U,2849
 brkraw/apps/loader/info/scan.yaml,sha256=tYyGRg4t_rf6jGZAT8F0_dUA9MlQeZ5zeOuTNQ2wQM8,1728
@@ -25,13 +25,13 @@ brkraw/cli/utils.py,sha256=Ii14ZqIVqDx-pIrRAtBrL50yzfEQcQZRtJSRWZ211mE,1348
 brkraw/cli/commands/__init__.py,sha256=PHh4jqD7i0aL8W8hXThczKcT4xsNZiXanBxOH5IOW5I,36
 brkraw/cli/commands/addon.py,sha256=yUK30gQ0AGse1WDifW5DLUCg84RlWGemid0uNVOnxzU,11179
 brkraw/cli/commands/config.py,sha256=bcbLQpb7Vw_imYwQsds4ZbWAOtgj_Dw3ojmFN4UmMBs,6471
-brkraw/cli/commands/convert.py,sha256=8mkJYZCFXKahqqOIN_C4W7F_qbcwR0idYy40cdhZILU,30615
-brkraw/cli/commands/hook.py,sha256=nPGIVMlWrpIJDCMdJABKGzV4HcuBdC3bLIh8cqJ8He4,11925
+brkraw/cli/commands/convert.py,sha256=FCnAcfQeiaTfckcffNVeUM3nDz1jSDutxYEnArgfxyM,30112
+brkraw/cli/commands/hook.py,sha256=_H0ielOlO_HwcvZTIsN5Gj32UivHUjRpKNgdlqjVrVg,11889
 brkraw/cli/commands/info.py,sha256=fwojS5GlEf2upY3v5-ueQQQf9CPWTn46-1-tub2gnxQ,2251
 brkraw/cli/commands/init.py,sha256=FLOimOmZbkrCRjTm0iJ8_w8o027He5dzbl3UT2Zu72U,6957
 brkraw/cli/commands/params.py,sha256=5z_2O24IrUL-_AEjHIzjZHA_89piDHtXkxHkd7C12D0,3159
 brkraw/cli/commands/prune.py,sha256=Sl8Zl78PAGtRvDB6HH-CqcDr4NBfXSrf8602ZAKL7nM,8798
-brkraw/cli/commands/session.py,sha256=COEjRwy-Z-Y9_-SZVAwUsIpDutXQ0UQ1baMNvjN6jYU,12749
+brkraw/cli/commands/session.py,sha256=t77PyNZpQoXxpszpqiKsOsKfLg9woXBJA_yinVhuEVk,12299
 brkraw/core/__init__.py,sha256=9UPOF5mtjZdGgjQ6-JJJs-eg8CGl4BuV7flGDWKgCBg,218
 brkraw/core/config.py,sha256=fohxJOoBruBrdzFIrXmBmZE5AW9EpnTOLAr3am8xDM8,11820
 brkraw/core/entrypoints.py,sha256=OqEvqBna7fTjR8MofIGJE80EzxL0WUYxeiJEUlQjfR8,880
@@ -57,12 +57,12 @@ brkraw/resolver/datatype.py,sha256=Kp-_-_JDfCh4io19Vw4YiAVTjWgaFAkxkO7ZDDglAKY,2
 brkraw/resolver/fid.py,sha256=SXglNSD6hFK7pAoHrUvuNbCYPgIAvbRdh6PACp7Oz7g,2847
 brkraw/resolver/helpers.py,sha256=BpL-zpbtGae6n-XQOmD5qP7KrD5HFnElzAD3bcBq0J4,1029
 brkraw/resolver/image.py,sha256=01mqBVFfoY2Z0V60k3G0qTKpEH-lqRCaSdkZ7pj7Bb8,6735
-brkraw/resolver/nifti.py,sha256=otqjDeRZMpplC6Z_uxWMjKoNtxvQyELvwK-ZbVMTuf8,12870
+brkraw/resolver/nifti.py,sha256=S4Z1NZdJp0LbipyUndEUoJqQzAjGfoizhGQC9byQG38,12617
 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
 brkraw/schema/meta.yaml,sha256=ePnTt7jD00lMKob6MPoziws9eYOWa-BX2MrVrIMSo90,1042
-brkraw/schema/niftiheader.yaml,sha256=Hj7eQNyLbyuT__-jznzAB15JIP9ArRhBGvJstZFGNZg,1499
+brkraw/schema/niftiheader.yaml,sha256=DmxhD6MUSdWb-aloXn3p4KNqqgWx_UVMqXsTJCQkYdw,1471
 brkraw/schema/pruner.yaml,sha256=bTmxvs5naAt_CsPQC-nIUEF5aL2T-iWUWGhg05ug_Ic,1023
 brkraw/schema/remapper.yaml,sha256=qIGiT6DqrJ2AK8g7gHj7Cc6GmQIT47VPaB2nRvnNc8k,3622
 brkraw/schema/rules.yaml,sha256=G9iOoy6B4yyzCAOVpinrrHSXa9QMJj0U_fY8C_mCq7I,2901
@@ -81,8 +81,8 @@ 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=w-NstF6o91EfLU2Ho00i8kbvvd7d8yrinPd83UnAW2c,9175
 brkraw/specs/rules/validator.py,sha256=AHS-r-E0HGHxwhhU48nCyS6LQvllQCgXLS_NDXBm3-k,3508
-brkraw-0.5.1.dist-info/METADATA,sha256=D6mXGLxZbPvEs1uW1GNaqzGi6fmN9DJvpD0eY3KejEY,3075
-brkraw-0.5.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-brkraw-0.5.1.dist-info/entry_points.txt,sha256=Qd3qG3g8GmGZUlV0gUP7WVpN_ulVn8Qw3l-O-stWxO0,450
-brkraw-0.5.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-brkraw-0.5.1.dist-info/RECORD,,
+brkraw-0.5.3.dist-info/METADATA,sha256=nV_JEoOsA59cI8cx87ACdxzhPmWYLFU6WqWX-5xNoq4,3068
+brkraw-0.5.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+brkraw-0.5.3.dist-info/entry_points.txt,sha256=Qd3qG3g8GmGZUlV0gUP7WVpN_ulVn8Qw3l-O-stWxO0,450
+brkraw-0.5.3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+brkraw-0.5.3.dist-info/RECORD,,