niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/register_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REGISTER_SUBJECT_METADATA = Metadata(
-    id="73901ff923fee339dbfc9565a4cb0066a06d8cbd.boutiques",
+    id="ee519dc7bfe305be35a0097fb38c1521d139695c.boutiques",
     name="register_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ REGISTER_SUBJECT_METADATA = Metadata(
 
 
 RegisterSubjectParameters = typing.TypedDict('RegisterSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["register_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/register_subject"]],
+    "input_volume": typing.NotRequired[InputPathType | None],
+    "mask_volume": typing.NotRequired[InputPathType | None],
+    "control_points": typing.NotRequired[str | None],
+    "output_directory": typing.NotRequired[str | None],
+    "log_file": typing.NotRequired[InputPathType | None],
+    "gca_file": typing.NotRequired[InputPathType | None],
+})
+RegisterSubjectParametersTagged = typing.TypedDict('RegisterSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/register_subject"],
     "input_volume": typing.NotRequired[InputPathType | None],
     "mask_volume": typing.NotRequired[InputPathType | None],
     "control_points": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ RegisterSubjectParameters = typing.TypedDict('RegisterSubjectParameters', {
     "log_file": typing.NotRequired[InputPathType | None],
     "gca_file": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "register_subject": register_subject_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "register_subject": register_subject_outputs,
-    }.get(t)
 
 
 class RegisterSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `register_subject(...)`.
+    Output object returned when calling `RegisterSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def register_subject_params(
     output_directory: str | None = None,
     log_file: InputPathType | None = None,
     gca_file: InputPathType | None = None,
-) -> RegisterSubjectParameters:
+) -> RegisterSubjectParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def register_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "register_subject",
+        "@type": "freesurfer/register_subject",
     }
     if input_volume is not None:
         params["input_volume"] = input_volume
@@ -123,18 +100,18 @@ def register_subject_cargs(
     """
     cargs = []
     cargs.append("register_subject")
-    if params.get("input_volume") is not None:
-        cargs.append(execution.input_file(params.get("input_volume")))
-    if params.get("mask_volume") is not None:
-        cargs.append(execution.input_file(params.get("mask_volume")))
-    if params.get("control_points") is not None:
-        cargs.append(params.get("control_points"))
-    if params.get("output_directory") is not None:
-        cargs.append(params.get("output_directory"))
-    if params.get("log_file") is not None:
-        cargs.append(execution.input_file(params.get("log_file")))
-    if params.get("gca_file") is not None:
-        cargs.append(execution.input_file(params.get("gca_file")))
+    if params.get("input_volume", None) is not None:
+        cargs.append(execution.input_file(params.get("input_volume", None)))
+    if params.get("mask_volume", None) is not None:
+        cargs.append(execution.input_file(params.get("mask_volume", None)))
+    if params.get("control_points", None) is not None:
+        cargs.append(params.get("control_points", None))
+    if params.get("output_directory", None) is not None:
+        cargs.append(params.get("output_directory", None))
+    if params.get("log_file", None) is not None:
+        cargs.append(execution.input_file(params.get("log_file", None)))
+    if params.get("gca_file", None) is not None:
+        cargs.append(execution.input_file(params.get("gca_file", None)))
     return cargs
 
 
@@ -153,17 +130,19 @@ def register_subject_outputs(
     """
     ret = RegisterSubjectOutputs(
         root=execution.output_file("."),
-        normalized_output=execution.output_file(params.get("output_directory") + "/norm.mgz") if (params.get("output_directory") is not None) else None,
-        transformed_fsamples=execution.output_file(params.get("output_directory") + "/fsamples") if (params.get("output_directory") is not None) else None,
+        normalized_output=execution.output_file(params.get("output_directory", None) + "/norm.mgz") if (params.get("output_directory") is not None) else None,
+        transformed_fsamples=execution.output_file(params.get("output_directory", None) + "/fsamples") if (params.get("output_directory") is not None) else None,
     )
     return ret
 
 
 def register_subject_execute(
     params: RegisterSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RegisterSubjectOutputs:
     """
+    register_subject
+    
     Tool for registering brain MR volumes.
     
     Author: FreeSurfer Developers
@@ -172,10 +151,12 @@ def register_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RegisterSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REGISTER_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = register_subject_cargs(params, execution)
     ret = register_subject_outputs(params, execution)
@@ -193,6 +174,8 @@ def register_subject(
     runner: Runner | None = None,
 ) -> RegisterSubjectOutputs:
     """
+    register_subject
+    
     Tool for registering brain MR volumes.
     
     Author: FreeSurfer Developers
@@ -211,8 +194,6 @@ def register_subject(
     Returns:
         NamedTuple of outputs (described in `RegisterSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REGISTER_SUBJECT_METADATA)
     params = register_subject_params(
         input_volume=input_volume,
         mask_volume=mask_volume,
@@ -221,13 +202,13 @@ def register_subject(
         log_file=log_file,
         gca_file=gca_file,
     )
-    return register_subject_execute(params, execution)
+    return register_subject_execute(params, runner)
 
 
 __all__ = [
     "REGISTER_SUBJECT_METADATA",
     "RegisterSubjectOutputs",
-    "RegisterSubjectParameters",
     "register_subject",
+    "register_subject_execute",
     "register_subject_params",
 ]

niwrap_freesurfer/freesurfer/register_subject_flash.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REGISTER_SUBJECT_FLASH_METADATA = Metadata(
-    id="51006ee3d0d1f2d75a6010754f505ba7fea67db5.boutiques",
+    id="1ed90dd43edd8a69b7a2b058cf60374353f7809f.boutiques",
     name="register_subject_flash",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ REGISTER_SUBJECT_FLASH_METADATA = Metadata(
 
 
 RegisterSubjectFlashParameters = typing.TypedDict('RegisterSubjectFlashParameters', {
-    "__STYXTYPE__": typing.Literal["register_subject_flash"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/register_subject_flash"]],
+    "input_volumes": list[InputPathType],
+})
+RegisterSubjectFlashParametersTagged = typing.TypedDict('RegisterSubjectFlashParametersTagged', {
+    "@type": typing.Literal["freesurfer/register_subject_flash"],
     "input_volumes": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "register_subject_flash": register_subject_flash_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "register_subject_flash": register_subject_flash_outputs,
-    }.get(t)
 
 
 class RegisterSubjectFlashOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `register_subject_flash(...)`.
+    Output object returned when calling `RegisterSubjectFlashParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class RegisterSubjectFlashOutputs(typing.NamedTuple):
 
 def register_subject_flash_params(
     input_volumes: list[InputPathType],
-) -> RegisterSubjectFlashParameters:
+) -> RegisterSubjectFlashParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def register_subject_flash_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "register_subject_flash",
+        "@type": "freesurfer/register_subject_flash",
         "input_volumes": input_volumes,
     }
     return params
@@ -94,7 +66,7 @@ def register_subject_flash_cargs(
     """
     cargs = []
     cargs.append("register_subject_flash")
-    cargs.extend([execution.input_file(f) for f in params.get("input_volumes")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_volumes", None)])
     return cargs
 
 
@@ -120,9 +92,11 @@ def register_subject_flash_outputs(
 
 def register_subject_flash_execute(
     params: RegisterSubjectFlashParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RegisterSubjectFlashOutputs:
     """
+    register_subject_flash
+    
     Register subject using the FLASH forward model to predict intensity values.
     
     Author: FreeSurfer Developers
@@ -131,10 +105,12 @@ def register_subject_flash_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RegisterSubjectFlashOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REGISTER_SUBJECT_FLASH_METADATA)
     params = execution.params(params)
     cargs = register_subject_flash_cargs(params, execution)
     ret = register_subject_flash_outputs(params, execution)
@@ -147,6 +123,8 @@ def register_subject_flash(
     runner: Runner | None = None,
 ) -> RegisterSubjectFlashOutputs:
     """
+    register_subject_flash
+    
     Register subject using the FLASH forward model to predict intensity values.
     
     Author: FreeSurfer Developers
@@ -159,18 +137,16 @@ def register_subject_flash(
     Returns:
         NamedTuple of outputs (described in `RegisterSubjectFlashOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REGISTER_SUBJECT_FLASH_METADATA)
     params = register_subject_flash_params(
         input_volumes=input_volumes,
     )
-    return register_subject_flash_execute(params, execution)
+    return register_subject_flash_execute(params, runner)
 
 
 __all__ = [
     "REGISTER_SUBJECT_FLASH_METADATA",
     "RegisterSubjectFlashOutputs",
-    "RegisterSubjectFlashParameters",
     "register_subject_flash",
+    "register_subject_flash_execute",
     "register_subject_flash_params",
 ]

niwrap_freesurfer/freesurfer/reinflate_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REINFLATE_SUBJECT_METADATA = Metadata(
-    id="1e08a83747d403bdb6fd509a84d2ca27a452f873.boutiques",
+    id="6a5c35db013d2ffc8b4d41d8751880dc7ef2df8e.boutiques",
     name="reinflate_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ REINFLATE_SUBJECT_METADATA = Metadata(
 
 
 ReinflateSubjectParameters = typing.TypedDict('ReinflateSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["reinflate_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reinflate_subject"]],
+    "args": typing.NotRequired[str | None],
+})
+ReinflateSubjectParametersTagged = typing.TypedDict('ReinflateSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/reinflate_subject"],
     "args": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reinflate_subject": reinflate_subject_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class ReinflateSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reinflate_subject(...)`.
+    Output object returned when calling `ReinflateSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class ReinflateSubjectOutputs(typing.NamedTuple):
 
 def reinflate_subject_params(
     args: str | None = None,
-) -> ReinflateSubjectParameters:
+) -> ReinflateSubjectParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def reinflate_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reinflate_subject",
+        "@type": "freesurfer/reinflate_subject",
     }
     if args is not None:
         params["args"] = args
@@ -92,8 +65,8 @@ def reinflate_subject_cargs(
     """
     cargs = []
     cargs.append("reinflate_subject")
-    if params.get("args") is not None:
-        cargs.append(params.get("args"))
+    if params.get("args", None) is not None:
+        cargs.append(params.get("args", None))
     return cargs
 
 
@@ -118,9 +91,11 @@ def reinflate_subject_outputs(
 
 def reinflate_subject_execute(
     params: ReinflateSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReinflateSubjectOutputs:
     """
+    reinflate_subject
+    
     Tool for reinflating brain surfaces.
     
     Author: FreeSurfer Developers
@@ -129,10 +104,12 @@ def reinflate_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReinflateSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REINFLATE_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = reinflate_subject_cargs(params, execution)
     ret = reinflate_subject_outputs(params, execution)
@@ -145,6 +122,8 @@ def reinflate_subject(
     runner: Runner | None = None,
 ) -> ReinflateSubjectOutputs:
     """
+    reinflate_subject
+    
     Tool for reinflating brain surfaces.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def reinflate_subject(
     Returns:
         NamedTuple of outputs (described in `ReinflateSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REINFLATE_SUBJECT_METADATA)
     params = reinflate_subject_params(
         args=args,
     )
-    return reinflate_subject_execute(params, execution)
+    return reinflate_subject_execute(params, runner)
 
 
 __all__ = [
     "REINFLATE_SUBJECT_METADATA",
     "ReinflateSubjectOutputs",
-    "ReinflateSubjectParameters",
     "reinflate_subject",
+    "reinflate_subject_execute",
     "reinflate_subject_params",
 ]

niwrap_freesurfer/freesurfer/reinflate_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REINFLATE_SUBJECT_LH_METADATA = Metadata(
-    id="42bb32324b2005eaf17fd4aaa28dc1b4f5722181.boutiques",
+    id="b44f8e0b6c91f3d76057be20617633b088a74caa.boutiques",
     name="reinflate_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ REINFLATE_SUBJECT_LH_METADATA = Metadata(
 
 
 ReinflateSubjectLhParameters = typing.TypedDict('ReinflateSubjectLhParameters', {
-    "__STYXTYPE__": typing.Literal["reinflate_subject-lh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reinflate_subject-lh"]],
+    "subject_id": str,
+})
+ReinflateSubjectLhParametersTagged = typing.TypedDict('ReinflateSubjectLhParametersTagged', {
+    "@type": typing.Literal["freesurfer/reinflate_subject-lh"],
     "subject_id": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reinflate_subject-lh": reinflate_subject_lh_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "reinflate_subject-lh": reinflate_subject_lh_outputs,
-    }.get(t)
 
 
 class ReinflateSubjectLhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reinflate_subject_lh(...)`.
+    Output object returned when calling `ReinflateSubjectLhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class ReinflateSubjectLhOutputs(typing.NamedTuple):
 
 def reinflate_subject_lh_params(
     subject_id: str,
-) -> ReinflateSubjectLhParameters:
+) -> ReinflateSubjectLhParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def reinflate_subject_lh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reinflate_subject-lh",
+        "@type": "freesurfer/reinflate_subject-lh",
         "subject_id": subject_id,
     }
     return params
@@ -96,7 +68,7 @@ def reinflate_subject_lh_cargs(
     cargs.append("reinflate_subject-lh")
     cargs.extend([
         "-lh",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     return cargs
 
@@ -116,16 +88,18 @@ def reinflate_subject_lh_outputs(
     """
     ret = ReinflateSubjectLhOutputs(
         root=execution.output_file("."),
-        inflated_surface=execution.output_file(params.get("subject_id") + "/surf/lh.inflated"),
+        inflated_surface=execution.output_file(params.get("subject_id", None) + "/surf/lh.inflated"),
     )
     return ret
 
 
 def reinflate_subject_lh_execute(
     params: ReinflateSubjectLhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReinflateSubjectLhOutputs:
     """
+    reinflate_subject-lh
+    
     Utility to reinflate cortical surfaces for left hemisphere in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -134,10 +108,12 @@ def reinflate_subject_lh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReinflateSubjectLhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REINFLATE_SUBJECT_LH_METADATA)
     params = execution.params(params)
     cargs = reinflate_subject_lh_cargs(params, execution)
     ret = reinflate_subject_lh_outputs(params, execution)
@@ -150,6 +126,8 @@ def reinflate_subject_lh(
     runner: Runner | None = None,
 ) -> ReinflateSubjectLhOutputs:
     """
+    reinflate_subject-lh
+    
     Utility to reinflate cortical surfaces for left hemisphere in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -162,18 +140,16 @@ def reinflate_subject_lh(
     Returns:
         NamedTuple of outputs (described in `ReinflateSubjectLhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REINFLATE_SUBJECT_LH_METADATA)
     params = reinflate_subject_lh_params(
         subject_id=subject_id,
     )
-    return reinflate_subject_lh_execute(params, execution)
+    return reinflate_subject_lh_execute(params, runner)
 
 
 __all__ = [
     "REINFLATE_SUBJECT_LH_METADATA",
     "ReinflateSubjectLhOutputs",
-    "ReinflateSubjectLhParameters",
     "reinflate_subject_lh",
+    "reinflate_subject_lh_execute",
     "reinflate_subject_lh_params",
 ]