niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/ico_supersample.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ICO_SUPERSAMPLE_METADATA = Metadata(
-    id="a325b40c5e9a6433abb23e27b0d456238f472064.boutiques",
+    id="afdc2214ca88f6905d69becf40fba25d4f48edea.boutiques",
     name="ico_supersample",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ ICO_SUPERSAMPLE_METADATA = Metadata(
 
 
 IcoSupersampleParameters = typing.TypedDict('IcoSupersampleParameters', {
-    "__STYXTYPE__": typing.Literal["ico_supersample"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/ico_supersample"]],
+    "refine": bool,
+    "radius": typing.NotRequired[float | None],
+    "projection_point": typing.NotRequired[list[float] | None],
+})
+IcoSupersampleParametersTagged = typing.TypedDict('IcoSupersampleParametersTagged', {
+    "@type": typing.Literal["freesurfer/ico_supersample"],
     "refine": bool,
     "radius": typing.NotRequired[float | None],
     "projection_point": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ico_supersample": ico_supersample_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 {
-        "ico_supersample": ico_supersample_outputs,
-    }.get(t)
 
 
 class IcoSupersampleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `ico_supersample(...)`.
+    Output object returned when calling `IcoSupersampleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def ico_supersample_params(
     refine: bool = False,
     radius: float | None = None,
     projection_point: list[float] | None = None,
-) -> IcoSupersampleParameters:
+) -> IcoSupersampleParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def ico_supersample_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ico_supersample",
+        "@type": "freesurfer/ico_supersample",
         "refine": refine,
     }
     if radius is not None:
@@ -105,12 +79,12 @@ def ico_supersample_cargs(
     """
     cargs = []
     cargs.append("ico_supersample")
-    if params.get("refine"):
+    if params.get("refine", False):
         cargs.append("-y")
-    if params.get("radius") is not None:
-        cargs.append(str(params.get("radius")))
-    if params.get("projection_point") is not None:
-        cargs.extend(map(str, params.get("projection_point")))
+    if params.get("radius", None) is not None:
+        cargs.append(str(params.get("radius", None)))
+    if params.get("projection_point", None) is not None:
+        cargs.extend(map(str, params.get("projection_point", None)))
     return cargs
 
 
@@ -136,9 +110,11 @@ def ico_supersample_outputs(
 
 def ico_supersample_execute(
     params: IcoSupersampleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IcoSupersampleOutputs:
     """
+    ico_supersample
+    
     A tool for refining icosahedron meshes with user-specified parameters.
     
     Author: FreeSurfer Developers
@@ -147,10 +123,12 @@ def ico_supersample_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IcoSupersampleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ICO_SUPERSAMPLE_METADATA)
     params = execution.params(params)
     cargs = ico_supersample_cargs(params, execution)
     ret = ico_supersample_outputs(params, execution)
@@ -165,6 +143,8 @@ def ico_supersample(
     runner: Runner | None = None,
 ) -> IcoSupersampleOutputs:
     """
+    ico_supersample
+    
     A tool for refining icosahedron meshes with user-specified parameters.
     
     Author: FreeSurfer Developers
@@ -180,20 +160,18 @@ def ico_supersample(
     Returns:
         NamedTuple of outputs (described in `IcoSupersampleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ICO_SUPERSAMPLE_METADATA)
     params = ico_supersample_params(
         refine=refine,
         radius=radius,
         projection_point=projection_point,
     )
-    return ico_supersample_execute(params, execution)
+    return ico_supersample_execute(params, runner)
 
 
 __all__ = [
     "ICO_SUPERSAMPLE_METADATA",
     "IcoSupersampleOutputs",
-    "IcoSupersampleParameters",
     "ico_supersample",
+    "ico_supersample_execute",
     "ico_supersample_params",
 ]

niwrap_freesurfer/freesurfer/ifh2hdr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IFH2HDR_METADATA = Metadata(
-    id="e59ad437a43879fdeda8a194eb2d5e26f853b35c.boutiques",
+    id="53f38f2257522a311eff6febece86eb780805751.boutiques",
     name="ifh2hdr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ IFH2HDR_METADATA = Metadata(
 
 
 Ifh2hdrParameters = typing.TypedDict('Ifh2hdrParameters', {
-    "__STYXTYPE__": typing.Literal["ifh2hdr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/ifh2hdr"]],
+    "input_file": InputPathType,
+    "range": typing.NotRequired[str | None],
+})
+Ifh2hdrParametersTagged = typing.TypedDict('Ifh2hdrParametersTagged', {
+    "@type": typing.Literal["freesurfer/ifh2hdr"],
     "input_file": InputPathType,
     "range": 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 {
-        "ifh2hdr": ifh2hdr_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 Ifh2hdrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `ifh2hdr(...)`.
+    Output object returned when calling `Ifh2hdrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class Ifh2hdrOutputs(typing.NamedTuple):
 def ifh2hdr_params(
     input_file: InputPathType,
     range_: str | None = None,
-) -> Ifh2hdrParameters:
+) -> Ifh2hdrParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def ifh2hdr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ifh2hdr",
+        "@type": "freesurfer/ifh2hdr",
         "input_file": input_file,
     }
     if range_ is not None:
@@ -96,11 +70,11 @@ def ifh2hdr_cargs(
     """
     cargs = []
     cargs.append("ifh2hdr")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("range") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("range", None) is not None:
         cargs.extend([
             "-r",
-            params.get("range")
+            params.get("range", None)
         ])
     return cargs
 
@@ -126,9 +100,11 @@ def ifh2hdr_outputs(
 
 def ifh2hdr_execute(
     params: Ifh2hdrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Ifh2hdrOutputs:
     """
+    ifh2hdr
+    
     Tool for converting IFH (Interfile Header) to HDR (Header) format in 4dfp
     (Four-Dimensional Functional Image) file format.
     
@@ -138,10 +114,12 @@ def ifh2hdr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Ifh2hdrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IFH2HDR_METADATA)
     params = execution.params(params)
     cargs = ifh2hdr_cargs(params, execution)
     ret = ifh2hdr_outputs(params, execution)
@@ -155,6 +133,8 @@ def ifh2hdr(
     runner: Runner | None = None,
 ) -> Ifh2hdrOutputs:
     """
+    ifh2hdr
+    
     Tool for converting IFH (Interfile Header) to HDR (Header) format in 4dfp
     (Four-Dimensional Functional Image) file format.
     
@@ -169,19 +149,17 @@ def ifh2hdr(
     Returns:
         NamedTuple of outputs (described in `Ifh2hdrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IFH2HDR_METADATA)
     params = ifh2hdr_params(
         input_file=input_file,
         range_=range_,
     )
-    return ifh2hdr_execute(params, execution)
+    return ifh2hdr_execute(params, runner)
 
 
 __all__ = [
     "IFH2HDR_METADATA",
     "Ifh2hdrOutputs",
-    "Ifh2hdrParameters",
     "ifh2hdr",
+    "ifh2hdr_execute",
     "ifh2hdr_params",
 ]

niwrap_freesurfer/freesurfer/imgreg_4dfp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMGREG_4DFP_METADATA = Metadata(
-    id="56f755f16ccfb6ca990d0bdefae3bf38a4194227.boutiques",
+    id="6dda694b6facf2585e8dfb06ba610f35b14226c8.boutiques",
     name="imgreg_4dfp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ IMGREG_4DFP_METADATA = Metadata(
 
 
 Imgreg4dfpParameters = typing.TypedDict('Imgreg4dfpParameters', {
-    "__STYXTYPE__": typing.Literal["imgreg_4dfp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/imgreg_4dfp"]],
+    "target_image": InputPathType,
+    "target_mask": str,
+    "source_image": InputPathType,
+    "source_mask": str,
+    "t4file": str,
+    "mode": str,
+})
+Imgreg4dfpParametersTagged = typing.TypedDict('Imgreg4dfpParametersTagged', {
+    "@type": typing.Literal["freesurfer/imgreg_4dfp"],
     "target_image": InputPathType,
     "target_mask": str,
     "source_image": InputPathType,
@@ -22,42 +31,11 @@ Imgreg4dfpParameters = typing.TypedDict('Imgreg4dfpParameters', {
     "t4file": str,
     "mode": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "imgreg_4dfp": imgreg_4dfp_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 Imgreg4dfpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `imgreg_4dfp(...)`.
+    Output object returned when calling `Imgreg4dfpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def imgreg_4dfp_params(
     mode: str,
     target_mask: str = "none",
     source_mask: str = "none",
-) -> Imgreg4dfpParameters:
+) -> Imgreg4dfpParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def imgreg_4dfp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "imgreg_4dfp",
+        "@type": "freesurfer/imgreg_4dfp",
         "target_image": target_image,
         "target_mask": target_mask,
         "source_image": source_image,
@@ -111,12 +89,12 @@ def imgreg_4dfp_cargs(
     """
     cargs = []
     cargs.append("imgreg_4dfp")
-    cargs.append(execution.input_file(params.get("target_image")))
-    cargs.append(params.get("target_mask"))
-    cargs.append(execution.input_file(params.get("source_image")))
-    cargs.append(params.get("source_mask"))
-    cargs.append(params.get("t4file"))
-    cargs.append(params.get("mode"))
+    cargs.append(execution.input_file(params.get("target_image", None)))
+    cargs.append(params.get("target_mask", "none"))
+    cargs.append(execution.input_file(params.get("source_image", None)))
+    cargs.append(params.get("source_mask", "none"))
+    cargs.append(params.get("t4file", None))
+    cargs.append(params.get("mode", None))
     return cargs
 
 
@@ -141,9 +119,11 @@ def imgreg_4dfp_outputs(
 
 def imgreg_4dfp_execute(
     params: Imgreg4dfpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Imgreg4dfpOutputs:
     """
+    imgreg_4dfp
+    
     Image registration utility using 4dfp.
     
     Author: FreeSurfer Developers
@@ -152,10 +132,12 @@ def imgreg_4dfp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Imgreg4dfpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMGREG_4DFP_METADATA)
     params = execution.params(params)
     cargs = imgreg_4dfp_cargs(params, execution)
     ret = imgreg_4dfp_outputs(params, execution)
@@ -173,6 +155,8 @@ def imgreg_4dfp(
     runner: Runner | None = None,
 ) -> Imgreg4dfpOutputs:
     """
+    imgreg_4dfp
+    
     Image registration utility using 4dfp.
     
     Author: FreeSurfer Developers
@@ -190,8 +174,6 @@ def imgreg_4dfp(
     Returns:
         NamedTuple of outputs (described in `Imgreg4dfpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IMGREG_4DFP_METADATA)
     params = imgreg_4dfp_params(
         target_image=target_image,
         target_mask=target_mask,
@@ -200,13 +182,13 @@ def imgreg_4dfp(
         t4file=t4file,
         mode=mode,
     )
-    return imgreg_4dfp_execute(params, execution)
+    return imgreg_4dfp_execute(params, runner)
 
 
 __all__ = [
     "IMGREG_4DFP_METADATA",
     "Imgreg4dfpOutputs",
-    "Imgreg4dfpParameters",
     "imgreg_4dfp",
+    "imgreg_4dfp_execute",
     "imgreg_4dfp_params",
 ]

niwrap_freesurfer/freesurfer/inflate_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_METADATA = Metadata(
-    id="ba316f47f940dcbc35fc9f6c2b7bf56afcc47cd8.boutiques",
+    id="6029c2b4a651632f9eac7ca7ed954a7f944c2c59.boutiques",
     name="inflate_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ INFLATE_SUBJECT_METADATA = Metadata(
 
 
 InflateSubjectParameters = typing.TypedDict('InflateSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["inflate_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/inflate_subject"]],
+    "args": typing.NotRequired[str | None],
+})
+InflateSubjectParametersTagged = typing.TypedDict('InflateSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/inflate_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 {
-        "inflate_subject": inflate_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 {
-        "inflate_subject": inflate_subject_outputs,
-    }.get(t)
 
 
 class InflateSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `inflate_subject(...)`.
+    Output object returned when calling `InflateSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class InflateSubjectOutputs(typing.NamedTuple):
 
 def inflate_subject_params(
     args: str | None = None,
-) -> InflateSubjectParameters:
+) -> InflateSubjectParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def inflate_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "inflate_subject",
+        "@type": "freesurfer/inflate_subject",
     }
     if args is not None:
         params["args"] = args
@@ -95,8 +67,8 @@ def inflate_subject_cargs(
     """
     cargs = []
     cargs.append("inflate_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
 
 
@@ -115,16 +87,18 @@ def inflate_subject_outputs(
     """
     ret = InflateSubjectOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("args") + "_output.txt") if (params.get("args") is not None) else None,
+        output_file=execution.output_file(params.get("args", None) + "_output.txt") if (params.get("args") is not None) else None,
     )
     return ret
 
 
 def inflate_subject_execute(
     params: InflateSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> InflateSubjectOutputs:
     """
+    inflate_subject
+    
     Inflate subject script for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -133,10 +107,12 @@ def inflate_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InflateSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = inflate_subject_cargs(params, execution)
     ret = inflate_subject_outputs(params, execution)
@@ -149,6 +125,8 @@ def inflate_subject(
     runner: Runner | None = None,
 ) -> InflateSubjectOutputs:
     """
+    inflate_subject
+    
     Inflate subject script for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -161,18 +139,16 @@ def inflate_subject(
     Returns:
         NamedTuple of outputs (described in `InflateSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(INFLATE_SUBJECT_METADATA)
     params = inflate_subject_params(
         args=args,
     )
-    return inflate_subject_execute(params, execution)
+    return inflate_subject_execute(params, runner)
 
 
 __all__ = [
     "INFLATE_SUBJECT_METADATA",
     "InflateSubjectOutputs",
-    "InflateSubjectParameters",
     "inflate_subject",
+    "inflate_subject_execute",
     "inflate_subject_params",
 ]