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

niwrap_freesurfer/freesurfer/reinflate_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REINFLATE_SUBJECT_RH_METADATA = Metadata(
-    id="9cd92db80be80b0a27f77251253c9b44f8012411.boutiques",
+    id="8d00ab3e958503c8e81a9bba5b706de4a1f36f3e.boutiques",
     name="reinflate_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ REINFLATE_SUBJECT_RH_METADATA = Metadata(
 
 
 ReinflateSubjectRhParameters = typing.TypedDict('ReinflateSubjectRhParameters', {
-    "__STYXTYPE__": typing.Literal["reinflate_subject-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reinflate_subject-rh"]],
+    "subject_dir": str,
+    "additional_options": typing.NotRequired[str | None],
+})
+ReinflateSubjectRhParametersTagged = typing.TypedDict('ReinflateSubjectRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/reinflate_subject-rh"],
     "subject_dir": str,
     "additional_options": 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-rh": reinflate_subject_rh_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 ReinflateSubjectRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reinflate_subject_rh(...)`.
+    Output object returned when calling `ReinflateSubjectRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class ReinflateSubjectRhOutputs(typing.NamedTuple):
 def reinflate_subject_rh_params(
     subject_dir: str,
     additional_options: str | None = None,
-) -> ReinflateSubjectRhParameters:
+) -> ReinflateSubjectRhParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def reinflate_subject_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reinflate_subject-rh",
+        "@type": "freesurfer/reinflate_subject-rh",
         "subject_dir": subject_dir,
     }
     if additional_options is not None:
@@ -99,10 +73,10 @@ def reinflate_subject_rh_cargs(
     cargs.append("reinflate_subject-rh")
     cargs.extend([
         "-rh",
-        params.get("subject_dir")
+        params.get("subject_dir", None)
     ])
-    if params.get("additional_options") is not None:
-        cargs.append(params.get("additional_options"))
+    if params.get("additional_options", None) is not None:
+        cargs.append(params.get("additional_options", None))
     return cargs
 
 
@@ -127,11 +101,13 @@ def reinflate_subject_rh_outputs(
 
 def reinflate_subject_rh_execute(
     params: ReinflateSubjectRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReinflateSubjectRhOutputs:
     """
-    A tool for reinflating the cortical surfaces for a given subject in FreeSurfer,
-    specifically for the right hemisphere.
+    reinflate_subject-rh
+    
+    A tool for reinflating the cortical surfaces for a given subject in
+    FreeSurfer, specifically for the right hemisphere.
     
     Author: FreeSurfer Developers
     
@@ -139,10 +115,12 @@ def reinflate_subject_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReinflateSubjectRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REINFLATE_SUBJECT_RH_METADATA)
     params = execution.params(params)
     cargs = reinflate_subject_rh_cargs(params, execution)
     ret = reinflate_subject_rh_outputs(params, execution)
@@ -156,8 +134,10 @@ def reinflate_subject_rh(
     runner: Runner | None = None,
 ) -> ReinflateSubjectRhOutputs:
     """
-    A tool for reinflating the cortical surfaces for a given subject in FreeSurfer,
-    specifically for the right hemisphere.
+    reinflate_subject-rh
+    
+    A tool for reinflating the cortical surfaces for a given subject in
+    FreeSurfer, specifically for the right hemisphere.
     
     Author: FreeSurfer Developers
     
@@ -171,19 +151,17 @@ def reinflate_subject_rh(
     Returns:
         NamedTuple of outputs (described in `ReinflateSubjectRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REINFLATE_SUBJECT_RH_METADATA)
     params = reinflate_subject_rh_params(
         subject_dir=subject_dir,
         additional_options=additional_options,
     )
-    return reinflate_subject_rh_execute(params, execution)
+    return reinflate_subject_rh_execute(params, runner)
 
 
 __all__ = [
     "REINFLATE_SUBJECT_RH_METADATA",
     "ReinflateSubjectRhOutputs",
-    "ReinflateSubjectRhParameters",
     "reinflate_subject_rh",
+    "reinflate_subject_rh_execute",
     "reinflate_subject_rh_params",
 ]

niwrap_freesurfer/freesurfer/remove_talairach.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REMOVE_TALAIRACH_METADATA = Metadata(
-    id="6d87145fdad666778dcc144dffa61059a2addded.boutiques",
+    id="980bfba14f04b23a9f4dac31030b29a4173a4cc5.boutiques",
     name="remove_talairach",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ REMOVE_TALAIRACH_METADATA = Metadata(
 
 
 RemoveTalairachParameters = typing.TypedDict('RemoveTalairachParameters', {
-    "__STYXTYPE__": typing.Literal["remove_talairach"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/remove_talairach"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+RemoveTalairachParametersTagged = typing.TypedDict('RemoveTalairachParametersTagged', {
+    "@type": typing.Literal["freesurfer/remove_talairach"],
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "remove_talairach": remove_talairach_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 {
-        "remove_talairach": remove_talairach_outputs,
-    }.get(t)
 
 
 class RemoveTalairachOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `remove_talairach(...)`.
+    Output object returned when calling `RemoveTalairachParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class RemoveTalairachOutputs(typing.NamedTuple):
 def remove_talairach_params(
     input_file: InputPathType,
     output_file: str,
-) -> RemoveTalairachParameters:
+) -> RemoveTalairachParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def remove_talairach_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "remove_talairach",
+        "@type": "freesurfer/remove_talairach",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -100,8 +73,8 @@ def remove_talairach_cargs(
     """
     cargs = []
     cargs.append("remove_talairach")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -120,16 +93,18 @@ def remove_talairach_outputs(
     """
     ret = RemoveTalairachOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("output_file")),
+        output_volume=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def remove_talairach_execute(
     params: RemoveTalairachParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RemoveTalairachOutputs:
     """
+    remove_talairach
+    
     A tool for removing the Talairach transformation from a volume.
     
     Author: FreeSurfer Developers
@@ -138,10 +113,12 @@ def remove_talairach_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RemoveTalairachOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REMOVE_TALAIRACH_METADATA)
     params = execution.params(params)
     cargs = remove_talairach_cargs(params, execution)
     ret = remove_talairach_outputs(params, execution)
@@ -155,6 +132,8 @@ def remove_talairach(
     runner: Runner | None = None,
 ) -> RemoveTalairachOutputs:
     """
+    remove_talairach
+    
     A tool for removing the Talairach transformation from a volume.
     
     Author: FreeSurfer Developers
@@ -170,19 +149,17 @@ def remove_talairach(
     Returns:
         NamedTuple of outputs (described in `RemoveTalairachOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REMOVE_TALAIRACH_METADATA)
     params = remove_talairach_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return remove_talairach_execute(params, execution)
+    return remove_talairach_execute(params, runner)
 
 
 __all__ = [
     "REMOVE_TALAIRACH_METADATA",
     "RemoveTalairachOutputs",
-    "RemoveTalairachParameters",
     "remove_talairach",
+    "remove_talairach_execute",
     "remove_talairach_params",
 ]

niwrap_freesurfer/freesurfer/renormalize_subject_keep_editting.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RENORMALIZE_SUBJECT_KEEP_EDITTING_METADATA = Metadata(
-    id="4fcb9d729e6622ba6a662eb312757c029ce1a009.boutiques",
+    id="b9c9ccbf63c872ce606e007e692c9ac397a167f4.boutiques",
     name="renormalize_subject_keep_editting",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ RENORMALIZE_SUBJECT_KEEP_EDITTING_METADATA = Metadata(
 
 
 RenormalizeSubjectKeepEdittingParameters = typing.TypedDict('RenormalizeSubjectKeepEdittingParameters', {
-    "__STYXTYPE__": typing.Literal["renormalize_subject_keep_editting"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/renormalize_subject_keep_editting"]],
+    "placeholder_input": typing.NotRequired[str | None],
+})
+RenormalizeSubjectKeepEdittingParametersTagged = typing.TypedDict('RenormalizeSubjectKeepEdittingParametersTagged', {
+    "@type": typing.Literal["freesurfer/renormalize_subject_keep_editting"],
     "placeholder_input": 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 {
-        "renormalize_subject_keep_editting": renormalize_subject_keep_editting_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 {
-        "renormalize_subject_keep_editting": renormalize_subject_keep_editting_outputs,
-    }.get(t)
 
 
 class RenormalizeSubjectKeepEdittingOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `renormalize_subject_keep_editting(...)`.
+    Output object returned when calling `RenormalizeSubjectKeepEdittingParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class RenormalizeSubjectKeepEdittingOutputs(typing.NamedTuple):
 
 def renormalize_subject_keep_editting_params(
     placeholder_input: str | None = None,
-) -> RenormalizeSubjectKeepEdittingParameters:
+) -> RenormalizeSubjectKeepEdittingParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +46,7 @@ def renormalize_subject_keep_editting_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "renormalize_subject_keep_editting",
+        "@type": "freesurfer/renormalize_subject_keep_editting",
     }
     if placeholder_input is not None:
         params["placeholder_input"] = placeholder_input
@@ -96,8 +68,8 @@ def renormalize_subject_keep_editting_cargs(
     """
     cargs = []
     cargs.append("renormalize_subject_keep_editting")
-    if params.get("placeholder_input") is not None:
-        cargs.append(params.get("placeholder_input"))
+    if params.get("placeholder_input", None) is not None:
+        cargs.append(params.get("placeholder_input", None))
     return cargs
 
 
@@ -123,9 +95,11 @@ def renormalize_subject_keep_editting_outputs(
 
 def renormalize_subject_keep_editting_execute(
     params: RenormalizeSubjectKeepEdittingParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RenormalizeSubjectKeepEdittingOutputs:
     """
+    renormalize_subject_keep_editting
+    
     A placeholder for the renormalize_subject_keep_editting tool, details not
     available.
     
@@ -135,10 +109,12 @@ def renormalize_subject_keep_editting_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RenormalizeSubjectKeepEdittingOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RENORMALIZE_SUBJECT_KEEP_EDITTING_METADATA)
     params = execution.params(params)
     cargs = renormalize_subject_keep_editting_cargs(params, execution)
     ret = renormalize_subject_keep_editting_outputs(params, execution)
@@ -151,6 +127,8 @@ def renormalize_subject_keep_editting(
     runner: Runner | None = None,
 ) -> RenormalizeSubjectKeepEdittingOutputs:
     """
+    renormalize_subject_keep_editting
+    
     A placeholder for the renormalize_subject_keep_editting tool, details not
     available.
     
@@ -165,18 +143,16 @@ def renormalize_subject_keep_editting(
     Returns:
         NamedTuple of outputs (described in `RenormalizeSubjectKeepEdittingOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RENORMALIZE_SUBJECT_KEEP_EDITTING_METADATA)
     params = renormalize_subject_keep_editting_params(
         placeholder_input=placeholder_input,
     )
-    return renormalize_subject_keep_editting_execute(params, execution)
+    return renormalize_subject_keep_editting_execute(params, runner)
 
 
 __all__ = [
     "RENORMALIZE_SUBJECT_KEEP_EDITTING_METADATA",
     "RenormalizeSubjectKeepEdittingOutputs",
-    "RenormalizeSubjectKeepEdittingParameters",
     "renormalize_subject_keep_editting",
+    "renormalize_subject_keep_editting_execute",
     "renormalize_subject_keep_editting_params",
 ]

niwrap_freesurfer/freesurfer/renormalize_t1_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RENORMALIZE_T1_SUBJECT_METADATA = Metadata(
-    id="fd1b560cfb5855fbdac004ecaa45cd6e0aa37abf.boutiques",
+    id="286fd25c6ee0546f2ffe25c3d4f9319f45adaa90.boutiques",
     name="renormalize_T1_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ RENORMALIZE_T1_SUBJECT_METADATA = Metadata(
 
 
 RenormalizeT1SubjectParameters = typing.TypedDict('RenormalizeT1SubjectParameters', {
-    "__STYXTYPE__": typing.Literal["renormalize_T1_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/renormalize_T1_subject"]],
+    "subject_dir": str,
+})
+RenormalizeT1SubjectParametersTagged = typing.TypedDict('RenormalizeT1SubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/renormalize_T1_subject"],
     "subject_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "renormalize_T1_subject": renormalize_t1_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 RenormalizeT1SubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `renormalize_t1_subject(...)`.
+    Output object returned when calling `RenormalizeT1SubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class RenormalizeT1SubjectOutputs(typing.NamedTuple):
 
 def renormalize_t1_subject_params(
     subject_dir: str,
-) -> RenormalizeT1SubjectParameters:
+) -> RenormalizeT1SubjectParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def renormalize_t1_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "renormalize_T1_subject",
+        "@type": "freesurfer/renormalize_T1_subject",
         "subject_dir": subject_dir,
     }
     return params
@@ -92,7 +65,7 @@ def renormalize_t1_subject_cargs(
     """
     cargs = []
     cargs.append("renormalize_T1_subject")
-    cargs.append(params.get("subject_dir"))
+    cargs.append(params.get("subject_dir", None))
     return cargs
 
 
@@ -117,9 +90,11 @@ def renormalize_t1_subject_outputs(
 
 def renormalize_t1_subject_execute(
     params: RenormalizeT1SubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RenormalizeT1SubjectOutputs:
     """
+    renormalize_T1_subject
+    
     Renormalize T1 subject images using FreeSurfer scripts.
     
     Author: FreeSurfer Developers
@@ -128,10 +103,12 @@ def renormalize_t1_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RenormalizeT1SubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RENORMALIZE_T1_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = renormalize_t1_subject_cargs(params, execution)
     ret = renormalize_t1_subject_outputs(params, execution)
@@ -144,6 +121,8 @@ def renormalize_t1_subject(
     runner: Runner | None = None,
 ) -> RenormalizeT1SubjectOutputs:
     """
+    renormalize_T1_subject
+    
     Renormalize T1 subject images using FreeSurfer scripts.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def renormalize_t1_subject(
     Returns:
         NamedTuple of outputs (described in `RenormalizeT1SubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RENORMALIZE_T1_SUBJECT_METADATA)
     params = renormalize_t1_subject_params(
         subject_dir=subject_dir,
     )
-    return renormalize_t1_subject_execute(params, execution)
+    return renormalize_t1_subject_execute(params, runner)
 
 
 __all__ = [
     "RENORMALIZE_T1_SUBJECT_METADATA",
     "RenormalizeT1SubjectOutputs",
-    "RenormalizeT1SubjectParameters",
     "renormalize_t1_subject",
+    "renormalize_t1_subject_execute",
     "renormalize_t1_subject_params",
 ]