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

niwrap_freesurfer/freesurfer/mris_volsmooth.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_VOLSMOOTH_METADATA = Metadata(
-    id="b95882126dfdb55e935d4a8cddda7e84c4e17f39.boutiques",
+    id="9803f4111198e4885811e3cd818e96b4c577f351.boutiques",
     name="mris_volsmooth",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ MRIS_VOLSMOOTH_METADATA = Metadata(
 
 
 MrisVolsmoothParameters = typing.TypedDict('MrisVolsmoothParameters', {
-    "__STYXTYPE__": typing.Literal["mris_volsmooth"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_volsmooth"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "registration": InputPathType,
+    "projfrac": typing.NotRequired[float | None],
+    "projfrac_avg": typing.NotRequired[str | None],
+    "fill_ribbon": bool,
+    "surf_out": typing.NotRequired[str | None],
+    "fwhm": typing.NotRequired[float | None],
+    "niters": typing.NotRequired[float | None],
+    "vol_fwhm": typing.NotRequired[float | None],
+    "log": typing.NotRequired[str | None],
+    "nocleanup": bool,
+    "debug": bool,
+})
+MrisVolsmoothParametersTagged = typing.TypedDict('MrisVolsmoothParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_volsmooth"],
     "input_volume": InputPathType,
     "output_volume": str,
     "registration": InputPathType,
@@ -29,43 +45,11 @@ MrisVolsmoothParameters = typing.TypedDict('MrisVolsmoothParameters', {
     "nocleanup": bool,
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_volsmooth": mris_volsmooth_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 {
-        "mris_volsmooth": mris_volsmooth_outputs,
-    }.get(t)
 
 
 class MrisVolsmoothOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_volsmooth(...)`.
+    Output object returned when calling `MrisVolsmoothParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +75,7 @@ def mris_volsmooth_params(
     log: str | None = None,
     nocleanup: bool = False,
     debug: bool = False,
-) -> MrisVolsmoothParameters:
+) -> MrisVolsmoothParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +102,7 @@ def mris_volsmooth_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_volsmooth",
+        "@type": "freesurfer/mris_volsmooth",
         "input_volume": input_volume,
         "output_volume": output_volume,
         "registration": registration,
@@ -160,56 +144,56 @@ def mris_volsmooth_cargs(
     cargs.append("mris_volsmooth")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
     cargs.extend([
         "-reg",
-        execution.input_file(params.get("registration"))
+        execution.input_file(params.get("registration", None))
     ])
-    if params.get("projfrac") is not None:
+    if params.get("projfrac", None) is not None:
         cargs.extend([
             "--projfrac",
-            str(params.get("projfrac"))
+            str(params.get("projfrac", None))
         ])
-    if params.get("projfrac_avg") is not None:
+    if params.get("projfrac_avg", None) is not None:
         cargs.extend([
             "--projfrac-avg",
-            params.get("projfrac_avg")
+            params.get("projfrac_avg", None)
         ])
-    if params.get("fill_ribbon"):
+    if params.get("fill_ribbon", False):
         cargs.append("--fill-ribbon")
-    if params.get("surf_out") is not None:
+    if params.get("surf_out", None) is not None:
         cargs.extend([
             "--surf-out",
-            params.get("surf_out")
+            params.get("surf_out", None)
         ])
-    if params.get("fwhm") is not None:
+    if params.get("fwhm", None) is not None:
         cargs.extend([
             "--fwhm",
-            str(params.get("fwhm"))
+            str(params.get("fwhm", None))
         ])
-    if params.get("niters") is not None:
+    if params.get("niters", None) is not None:
         cargs.extend([
             "--niters",
-            str(params.get("niters"))
+            str(params.get("niters", None))
         ])
-    if params.get("vol_fwhm") is not None:
+    if params.get("vol_fwhm", None) is not None:
         cargs.extend([
             "--vol-fwhm",
-            str(params.get("vol_fwhm"))
+            str(params.get("vol_fwhm", None))
         ])
-    if params.get("log") is not None:
+    if params.get("log", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log")
+            params.get("log", None)
         ])
-    if params.get("nocleanup"):
+    if params.get("nocleanup", False):
         cargs.append("--nocleanup")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -229,18 +213,20 @@ def mris_volsmooth_outputs(
     """
     ret = MrisVolsmoothOutputs(
         root=execution.output_file("."),
-        outvol_file=execution.output_file(params.get("output_volume") + ".mgh"),
-        lh_surface_output=execution.output_file(params.get("surf_out") + ".lh.mgh") if (params.get("surf_out") is not None) else None,
-        rh_surface_output=execution.output_file(params.get("surf_out") + ".rh.mgh") if (params.get("surf_out") is not None) else None,
+        outvol_file=execution.output_file(params.get("output_volume", None) + ".mgh"),
+        lh_surface_output=execution.output_file(params.get("surf_out", None) + ".lh.mgh") if (params.get("surf_out") is not None) else None,
+        rh_surface_output=execution.output_file(params.get("surf_out", None) + ".rh.mgh") if (params.get("surf_out") is not None) else None,
     )
     return ret
 
 
 def mris_volsmooth_execute(
     params: MrisVolsmoothParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisVolsmoothOutputs:
     """
+    mris_volsmooth
+    
     Performs surface-based smoothing inside a volume by sampling a volume to a
     surface, smoothing on the surface, then replacing the surface voxels in the
     volume with values that were smoothed.
@@ -251,10 +237,12 @@ def mris_volsmooth_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisVolsmoothOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_VOLSMOOTH_METADATA)
     params = execution.params(params)
     cargs = mris_volsmooth_cargs(params, execution)
     ret = mris_volsmooth_outputs(params, execution)
@@ -279,6 +267,8 @@ def mris_volsmooth(
     runner: Runner | None = None,
 ) -> MrisVolsmoothOutputs:
     """
+    mris_volsmooth
+    
     Performs surface-based smoothing inside a volume by sampling a volume to a
     surface, smoothing on the surface, then replacing the surface voxels in the
     volume with values that were smoothed.
@@ -310,8 +300,6 @@ def mris_volsmooth(
     Returns:
         NamedTuple of outputs (described in `MrisVolsmoothOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_VOLSMOOTH_METADATA)
     params = mris_volsmooth_params(
         input_volume=input_volume,
         output_volume=output_volume,
@@ -327,13 +315,13 @@ def mris_volsmooth(
         nocleanup=nocleanup,
         debug=debug,
     )
-    return mris_volsmooth_execute(params, execution)
+    return mris_volsmooth_execute(params, runner)
 
 
 __all__ = [
     "MRIS_VOLSMOOTH_METADATA",
     "MrisVolsmoothOutputs",
-    "MrisVolsmoothParameters",
     "mris_volsmooth",
+    "mris_volsmooth_execute",
     "mris_volsmooth_params",
 ]

niwrap_freesurfer/freesurfer/mris_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_VOLUME_METADATA = Metadata(
-    id="22120a055906c9c4c76b399c2a02bf0fd2a685bc.boutiques",
+    id="6ad4f96c9555477dc22b4f117fd35e0393cf71a5.boutiques",
     name="mris_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ MRIS_VOLUME_METADATA = Metadata(
 
 
 MrisVolumeParameters = typing.TypedDict('MrisVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["mris_volume"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_volume"]],
+    "surface_file": InputPathType,
+    "verbose_flag": bool,
+})
+MrisVolumeParametersTagged = typing.TypedDict('MrisVolumeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_volume"],
     "surface_file": InputPathType,
     "verbose_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_volume": mris_volume_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 MrisVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_volume(...)`.
+    Output object returned when calling `MrisVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class MrisVolumeOutputs(typing.NamedTuple):
 def mris_volume_params(
     surface_file: InputPathType,
     verbose_flag: bool = False,
-) -> MrisVolumeParameters:
+) -> MrisVolumeParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def mris_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_volume",
+        "@type": "freesurfer/mris_volume",
         "surface_file": surface_file,
         "verbose_flag": verbose_flag,
     }
@@ -95,8 +69,8 @@ def mris_volume_cargs(
     """
     cargs = []
     cargs.append("mris_volume")
-    cargs.append(execution.input_file(params.get("surface_file")))
-    if params.get("verbose_flag"):
+    cargs.append(execution.input_file(params.get("surface_file", None)))
+    if params.get("verbose_flag", False):
         cargs.append("-v")
     return cargs
 
@@ -122,10 +96,13 @@ def mris_volume_outputs(
 
 def mris_volume_execute(
     params: MrisVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisVolumeOutputs:
     """
-    A tool for computing the volume of a closed surface using a divergence formula.
+    mris_volume
+    
+    A tool for computing the volume of a closed surface using a divergence
+    formula.
     
     Author: FreeSurfer Developers
     
@@ -133,10 +110,12 @@ def mris_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_VOLUME_METADATA)
     params = execution.params(params)
     cargs = mris_volume_cargs(params, execution)
     ret = mris_volume_outputs(params, execution)
@@ -150,7 +129,10 @@ def mris_volume(
     runner: Runner | None = None,
 ) -> MrisVolumeOutputs:
     """
-    A tool for computing the volume of a closed surface using a divergence formula.
+    mris_volume
+    
+    A tool for computing the volume of a closed surface using a divergence
+    formula.
     
     Author: FreeSurfer Developers
     
@@ -163,19 +145,17 @@ def mris_volume(
     Returns:
         NamedTuple of outputs (described in `MrisVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_VOLUME_METADATA)
     params = mris_volume_params(
         surface_file=surface_file,
         verbose_flag=verbose_flag,
     )
-    return mris_volume_execute(params, execution)
+    return mris_volume_execute(params, runner)
 
 
 __all__ = [
     "MRIS_VOLUME_METADATA",
     "MrisVolumeOutputs",
-    "MrisVolumeParameters",
     "mris_volume",
+    "mris_volume_execute",
     "mris_volume_params",
 ]

niwrap_freesurfer/freesurfer/mris_warp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_WARP_METADATA = Metadata(
-    id="d4ff63326a23c044a153e9290787b0570c1455d8.boutiques",
+    id="e858eca5a999ef2c6d76f6c13248ad58052c6ec0.boutiques",
     name="mris_warp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRIS_WARP_METADATA = Metadata(
 
 
 MrisWarpParameters = typing.TypedDict('MrisWarpParameters', {
-    "__STYXTYPE__": typing.Literal["mris_warp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_warp"]],
+    "deformvol": typing.NotRequired[str | None],
+    "m3z": typing.NotRequired[str | None],
+    "regfile": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+    "out": typing.NotRequired[str | None],
+    "abs": bool,
+    "help": bool,
+    "version": bool,
+})
+MrisWarpParametersTagged = typing.TypedDict('MrisWarpParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_warp"],
     "deformvol": typing.NotRequired[str | None],
     "m3z": typing.NotRequired[str | None],
     "regfile": typing.NotRequired[str | None],
@@ -24,43 +35,11 @@ MrisWarpParameters = typing.TypedDict('MrisWarpParameters', {
     "help": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_warp": mris_warp_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 {
-        "mris_warp": mris_warp_outputs,
-    }.get(t)
 
 
 class MrisWarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_warp(...)`.
+    Output object returned when calling `MrisWarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def mris_warp_params(
     abs_: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> MrisWarpParameters:
+) -> MrisWarpParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def mris_warp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_warp",
+        "@type": "freesurfer/mris_warp",
         "abs": abs_,
         "help": help_,
         "version": version,
@@ -128,36 +107,36 @@ def mris_warp_cargs(
     """
     cargs = []
     cargs.append("mris_warp")
-    if params.get("deformvol") is not None:
+    if params.get("deformvol", None) is not None:
         cargs.extend([
             "--deformvol",
-            params.get("deformvol")
+            params.get("deformvol", None)
         ])
-    if params.get("m3z") is not None:
+    if params.get("m3z", None) is not None:
         cargs.extend([
             "--m3z",
-            params.get("m3z")
+            params.get("m3z", None)
         ])
-    if params.get("regfile") is not None:
+    if params.get("regfile", None) is not None:
         cargs.extend([
             "--reg",
-            params.get("regfile")
+            params.get("regfile", None)
         ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
-    if params.get("out") is not None:
+    if params.get("out", None) is not None:
         cargs.extend([
             "--out",
-            params.get("out")
+            params.get("out", None)
         ])
-    if params.get("abs"):
+    if params.get("abs", False):
         cargs.append("--abs")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -177,16 +156,18 @@ def mris_warp_outputs(
     """
     ret = MrisWarpOutputs(
         root=execution.output_file("."),
-        output_surface=execution.output_file(params.get("out")) if (params.get("out") is not None) else None,
+        output_surface=execution.output_file(params.get("out", None)) if (params.get("out") is not None) else None,
     )
     return ret
 
 
 def mris_warp_execute(
     params: MrisWarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisWarpOutputs:
     """
+    mris_warp
+    
     This program will warp a surface using a specified deformation field.
     
     Author: FreeSurfer Developers
@@ -195,10 +176,12 @@ def mris_warp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisWarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_WARP_METADATA)
     params = execution.params(params)
     cargs = mris_warp_cargs(params, execution)
     ret = mris_warp_outputs(params, execution)
@@ -218,6 +201,8 @@ def mris_warp(
     runner: Runner | None = None,
 ) -> MrisWarpOutputs:
     """
+    mris_warp
+    
     This program will warp a surface using a specified deformation field.
     
     Author: FreeSurfer Developers
@@ -238,8 +223,6 @@ def mris_warp(
     Returns:
         NamedTuple of outputs (described in `MrisWarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_WARP_METADATA)
     params = mris_warp_params(
         deformvol=deformvol,
         m3z=m3z,
@@ -250,13 +233,13 @@ def mris_warp(
         help_=help_,
         version=version,
     )
-    return mris_warp_execute(params, execution)
+    return mris_warp_execute(params, runner)
 
 
 __all__ = [
     "MRIS_WARP_METADATA",
     "MrisWarpOutputs",
-    "MrisWarpParameters",
     "mris_warp",
+    "mris_warp_execute",
     "mris_warp_params",
 ]