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

niwrap_freesurfer/freesurfer/mris_label_mode.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_LABEL_MODE_METADATA = Metadata(
-    id="591967f9eeb3bb3b9f31868769d0fb3d8379053f.boutiques",
+    id="6edab91d606ca7c4a36e17024963e26907e58292.boutiques",
     name="mris_label_mode",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRIS_LABEL_MODE_METADATA = Metadata(
 
 
 MrisLabelModeParameters = typing.TypedDict('MrisLabelModeParameters', {
-    "__STYXTYPE__": typing.Literal["mris_label_mode"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_label_mode"]],
+    "input_curv_file": InputPathType,
+    "hemi": str,
+    "surface": str,
+    "subject": list[str],
+    "output_curv_file": str,
+    "summary_statistics": bool,
+    "statistics_cond": typing.NotRequired[str | None],
+    "output_directory": typing.NotRequired[str | None],
+})
+MrisLabelModeParametersTagged = typing.TypedDict('MrisLabelModeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_label_mode"],
     "input_curv_file": InputPathType,
     "hemi": str,
     "surface": str,
@@ -24,42 +35,11 @@ MrisLabelModeParameters = typing.TypedDict('MrisLabelModeParameters', {
     "statistics_cond": typing.NotRequired[str | None],
     "output_directory": 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 {
-        "mris_label_mode": mris_label_mode_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 MrisLabelModeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_label_mode(...)`.
+    Output object returned when calling `MrisLabelModeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def mris_label_mode_params(
     summary_statistics: bool = False,
     statistics_cond: str | None = None,
     output_directory: str | None = None,
-) -> MrisLabelModeParameters:
+) -> MrisLabelModeParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def mris_label_mode_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_label_mode",
+        "@type": "freesurfer/mris_label_mode",
         "input_curv_file": input_curv_file,
         "hemi": hemi,
         "surface": surface,
@@ -121,19 +101,19 @@ def mris_label_mode_cargs(
     """
     cargs = []
     cargs.append("mris_label_mode")
-    cargs.append(execution.input_file(params.get("input_curv_file")))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface"))
-    cargs.extend(params.get("subject"))
-    cargs.append(params.get("output_curv_file"))
-    if params.get("summary_statistics"):
+    cargs.append(execution.input_file(params.get("input_curv_file", None)))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface", None))
+    cargs.extend(params.get("subject", None))
+    cargs.append(params.get("output_curv_file", None))
+    if params.get("summary_statistics", False):
         cargs.append("-s")
-    if params.get("statistics_cond") is not None:
-        cargs.append(params.get("statistics_cond"))
-    if params.get("output_directory") is not None:
+    if params.get("statistics_cond", None) is not None:
+        cargs.append(params.get("statistics_cond", None))
+    if params.get("output_directory", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_directory")
+            params.get("output_directory", None)
         ])
     return cargs
 
@@ -159,9 +139,11 @@ def mris_label_mode_outputs(
 
 def mris_label_mode_execute(
     params: MrisLabelModeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisLabelModeOutputs:
     """
+    mris_label_mode
+    
     This program will add a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -170,10 +152,12 @@ def mris_label_mode_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisLabelModeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_LABEL_MODE_METADATA)
     params = execution.params(params)
     cargs = mris_label_mode_cargs(params, execution)
     ret = mris_label_mode_outputs(params, execution)
@@ -193,6 +177,8 @@ def mris_label_mode(
     runner: Runner | None = None,
 ) -> MrisLabelModeOutputs:
     """
+    mris_label_mode
+    
     This program will add a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -212,8 +198,6 @@ def mris_label_mode(
     Returns:
         NamedTuple of outputs (described in `MrisLabelModeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_LABEL_MODE_METADATA)
     params = mris_label_mode_params(
         input_curv_file=input_curv_file,
         hemi=hemi,
@@ -224,13 +208,13 @@ def mris_label_mode(
         statistics_cond=statistics_cond,
         output_directory=output_directory,
     )
-    return mris_label_mode_execute(params, execution)
+    return mris_label_mode_execute(params, runner)
 
 
 __all__ = [
     "MRIS_LABEL_MODE_METADATA",
     "MrisLabelModeOutputs",
-    "MrisLabelModeParameters",
     "mris_label_mode",
+    "mris_label_mode_execute",
     "mris_label_mode_params",
 ]

niwrap_freesurfer/freesurfer/mris_left_right_register.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_LEFT_RIGHT_REGISTER_METADATA = Metadata(
-    id="e63f9c437139fff9b770440c97fbe2c2f184e3d5.boutiques",
+    id="deb90227cd838d310a8c1fb72cfbad83cbc6d25f.boutiques",
     name="mris_left_right_register",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_LEFT_RIGHT_REGISTER_METADATA = Metadata(
 
 
 MrisLeftRightRegisterParameters = typing.TypedDict('MrisLeftRightRegisterParameters', {
-    "__STYXTYPE__": typing.Literal["mris_left_right_register"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_left_right_register"]],
+    "lh_sphere": InputPathType,
+    "rh_sphere": InputPathType,
+    "lh_sphere_left_right": str,
+    "rh_sphere_left_right": str,
+})
+MrisLeftRightRegisterParametersTagged = typing.TypedDict('MrisLeftRightRegisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_left_right_register"],
     "lh_sphere": InputPathType,
     "rh_sphere": InputPathType,
     "lh_sphere_left_right": str,
     "rh_sphere_left_right": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_left_right_register": mris_left_right_register_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_left_right_register": mris_left_right_register_outputs,
-    }.get(t)
 
 
 class MrisLeftRightRegisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_left_right_register(...)`.
+    Output object returned when calling `MrisLeftRightRegisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +46,7 @@ def mris_left_right_register_params(
     rh_sphere: InputPathType,
     lh_sphere_left_right: str,
     rh_sphere_left_right: str,
-) -> MrisLeftRightRegisterParameters:
+) -> MrisLeftRightRegisterParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +61,7 @@ def mris_left_right_register_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_left_right_register",
+        "@type": "freesurfer/mris_left_right_register",
         "lh_sphere": lh_sphere,
         "rh_sphere": rh_sphere,
         "lh_sphere_left_right": lh_sphere_left_right,
@@ -110,10 +85,10 @@ def mris_left_right_register_cargs(
     """
     cargs = []
     cargs.append("mris_left_right_register")
-    cargs.append(execution.input_file(params.get("lh_sphere")))
-    cargs.append(execution.input_file(params.get("rh_sphere")))
-    cargs.append(params.get("lh_sphere_left_right"))
-    cargs.append(params.get("rh_sphere_left_right"))
+    cargs.append(execution.input_file(params.get("lh_sphere", None)))
+    cargs.append(execution.input_file(params.get("rh_sphere", None)))
+    cargs.append(params.get("lh_sphere_left_right", None))
+    cargs.append(params.get("rh_sphere_left_right", None))
     return cargs
 
 
@@ -132,17 +107,19 @@ def mris_left_right_register_outputs(
     """
     ret = MrisLeftRightRegisterOutputs(
         root=execution.output_file("."),
-        out_lh_sphere_left_right=execution.output_file(params.get("lh_sphere_left_right")),
-        out_rh_sphere_left_right=execution.output_file(params.get("rh_sphere_left_right")),
+        out_lh_sphere_left_right=execution.output_file(params.get("lh_sphere_left_right", None)),
+        out_rh_sphere_left_right=execution.output_file(params.get("rh_sphere_left_right", None)),
     )
     return ret
 
 
 def mris_left_right_register_execute(
     params: MrisLeftRightRegisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisLeftRightRegisterOutputs:
     """
+    mris_left_right_register
+    
     Register left and right hemisphere spherical surfaces.
     
     Author: FreeSurfer Developers
@@ -151,10 +128,12 @@ def mris_left_right_register_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisLeftRightRegisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_LEFT_RIGHT_REGISTER_METADATA)
     params = execution.params(params)
     cargs = mris_left_right_register_cargs(params, execution)
     ret = mris_left_right_register_outputs(params, execution)
@@ -170,6 +149,8 @@ def mris_left_right_register(
     runner: Runner | None = None,
 ) -> MrisLeftRightRegisterOutputs:
     """
+    mris_left_right_register
+    
     Register left and right hemisphere spherical surfaces.
     
     Author: FreeSurfer Developers
@@ -187,21 +168,19 @@ def mris_left_right_register(
     Returns:
         NamedTuple of outputs (described in `MrisLeftRightRegisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_LEFT_RIGHT_REGISTER_METADATA)
     params = mris_left_right_register_params(
         lh_sphere=lh_sphere,
         rh_sphere=rh_sphere,
         lh_sphere_left_right=lh_sphere_left_right,
         rh_sphere_left_right=rh_sphere_left_right,
     )
-    return mris_left_right_register_execute(params, execution)
+    return mris_left_right_register_execute(params, runner)
 
 
 __all__ = [
     "MRIS_LEFT_RIGHT_REGISTER_METADATA",
     "MrisLeftRightRegisterOutputs",
-    "MrisLeftRightRegisterParameters",
     "mris_left_right_register",
+    "mris_left_right_register_execute",
     "mris_left_right_register_params",
 ]

niwrap_freesurfer/freesurfer/mris_make_average_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MAKE_AVERAGE_SURFACE_METADATA = Metadata(
-    id="5ca60dd661acd09992cf09d60028e85c12fb8055.boutiques",
+    id="8e295710b170889abde16b3d1234bede6346e6ae.boutiques",
     name="mris_make_average_surface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ MRIS_MAKE_AVERAGE_SURFACE_METADATA = Metadata(
 
 
 MrisMakeAverageSurfaceParameters = typing.TypedDict('MrisMakeAverageSurfaceParameters', {
-    "__STYXTYPE__": typing.Literal["mris_make_average_surface"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_make_average_surface"]],
+    "hemi": str,
+    "outsurfname": str,
+    "cansurfname": str,
+    "outsubject": str,
+    "subjects": list[str],
+    "sdir": typing.NotRequired[str | None],
+    "sdir_out": typing.NotRequired[str | None],
+    "nonorm_flag": bool,
+    "icoorder": typing.NotRequired[float | None],
+    "xfmname": typing.NotRequired[str | None],
+    "templatename": typing.NotRequired[str | None],
+    "surfname": typing.NotRequired[str | None],
+    "surf2surf_flag": bool,
+    "simple": typing.NotRequired[list[str] | None],
+    "diagno": typing.NotRequired[float | None],
+})
+MrisMakeAverageSurfaceParametersTagged = typing.TypedDict('MrisMakeAverageSurfaceParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_make_average_surface"],
     "hemi": str,
     "outsurfname": str,
     "cansurfname": str,
@@ -31,43 +49,11 @@ MrisMakeAverageSurfaceParameters = typing.TypedDict('MrisMakeAverageSurfaceParam
     "simple": typing.NotRequired[list[str] | None],
     "diagno": typing.NotRequired[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 {
-        "mris_make_average_surface": mris_make_average_surface_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_make_average_surface": mris_make_average_surface_outputs,
-    }.get(t)
 
 
 class MrisMakeAverageSurfaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_make_average_surface(...)`.
+    Output object returned when calling `MrisMakeAverageSurfaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +77,7 @@ def mris_make_average_surface_params(
     surf2surf_flag: bool = False,
     simple: list[str] | None = None,
     diagno: float | None = None,
-) -> MrisMakeAverageSurfaceParameters:
+) -> MrisMakeAverageSurfaceParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +103,7 @@ def mris_make_average_surface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_make_average_surface",
+        "@type": "freesurfer/mris_make_average_surface",
         "hemi": hemi,
         "outsurfname": outsurfname,
         "cansurfname": cansurfname,
@@ -160,54 +146,54 @@ def mris_make_average_surface_cargs(
     """
     cargs = []
     cargs.append("mris_make_average_surface")
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("outsurfname"))
-    cargs.append(params.get("cansurfname"))
-    cargs.append(params.get("outsubject"))
-    cargs.extend(params.get("subjects"))
-    if params.get("sdir") is not None:
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("outsurfname", None))
+    cargs.append(params.get("cansurfname", None))
+    cargs.append(params.get("outsubject", None))
+    cargs.extend(params.get("subjects", None))
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("sdir_out") is not None:
+    if params.get("sdir_out", None) is not None:
         cargs.extend([
             "-sdir-out",
-            params.get("sdir_out")
+            params.get("sdir_out", None)
         ])
-    if params.get("nonorm_flag"):
+    if params.get("nonorm_flag", False):
         cargs.append("-nonorm")
-    if params.get("icoorder") is not None:
+    if params.get("icoorder", None) is not None:
         cargs.extend([
             "-i",
-            str(params.get("icoorder"))
+            str(params.get("icoorder", None))
         ])
-    if params.get("xfmname") is not None:
+    if params.get("xfmname", None) is not None:
         cargs.extend([
             "-x",
-            params.get("xfmname")
+            params.get("xfmname", None)
         ])
-    if params.get("templatename") is not None:
+    if params.get("templatename", None) is not None:
         cargs.extend([
             "-t",
-            params.get("templatename")
+            params.get("templatename", None)
         ])
-    if params.get("surfname") is not None:
+    if params.get("surfname", None) is not None:
         cargs.extend([
             "-s",
-            params.get("surfname")
+            params.get("surfname", None)
         ])
-    if params.get("surf2surf_flag"):
+    if params.get("surf2surf_flag", False):
         cargs.append("-surf2surf")
-    if params.get("simple") is not None:
+    if params.get("simple", None) is not None:
         cargs.extend([
             "-simple",
-            *params.get("simple")
+            *params.get("simple", None)
         ])
-    if params.get("diagno") is not None:
+    if params.get("diagno", None) is not None:
         cargs.extend([
             "-v",
-            str(params.get("diagno"))
+            str(params.get("diagno", None))
         ])
     return cargs
 
@@ -227,18 +213,20 @@ def mris_make_average_surface_outputs(
     """
     ret = MrisMakeAverageSurfaceOutputs(
         root=execution.output_file("."),
-        output_surface=execution.output_file(params.get("sdir_out") + "/" + params.get("outsubject") + "/" + params.get("outsurfname")) if (params.get("sdir_out") is not None) else None,
+        output_surface=execution.output_file(params.get("sdir_out", None) + "/" + params.get("outsubject", None) + "/" + params.get("outsurfname", None)) if (params.get("sdir_out") is not None) else None,
     )
     return ret
 
 
 def mris_make_average_surface_execute(
     params: MrisMakeAverageSurfaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMakeAverageSurfaceOutputs:
     """
-    A program to average the orig surfaces from the given subject list into a single
-    surface using Talairach coords and the spherical transform.
+    mris_make_average_surface
+    
+    A program to average the orig surfaces from the given subject list into a
+    single surface using Talairach coords and the spherical transform.
     
     Author: FreeSurfer Developers
     
@@ -246,10 +234,12 @@ def mris_make_average_surface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMakeAverageSurfaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MAKE_AVERAGE_SURFACE_METADATA)
     params = execution.params(params)
     cargs = mris_make_average_surface_cargs(params, execution)
     ret = mris_make_average_surface_outputs(params, execution)
@@ -276,8 +266,10 @@ def mris_make_average_surface(
     runner: Runner | None = None,
 ) -> MrisMakeAverageSurfaceOutputs:
     """
-    A program to average the orig surfaces from the given subject list into a single
-    surface using Talairach coords and the spherical transform.
+    mris_make_average_surface
+    
+    A program to average the orig surfaces from the given subject list into a
+    single surface using Talairach coords and the spherical transform.
     
     Author: FreeSurfer Developers
     
@@ -305,8 +297,6 @@ def mris_make_average_surface(
     Returns:
         NamedTuple of outputs (described in `MrisMakeAverageSurfaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MAKE_AVERAGE_SURFACE_METADATA)
     params = mris_make_average_surface_params(
         hemi=hemi,
         outsurfname=outsurfname,
@@ -324,13 +314,13 @@ def mris_make_average_surface(
         simple=simple,
         diagno=diagno,
     )
-    return mris_make_average_surface_execute(params, execution)
+    return mris_make_average_surface_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MAKE_AVERAGE_SURFACE_METADATA",
     "MrisMakeAverageSurfaceOutputs",
-    "MrisMakeAverageSurfaceParameters",
     "mris_make_average_surface",
+    "mris_make_average_surface_execute",
     "mris_make_average_surface_params",
 ]