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

niwrap_freesurfer/freesurfer/mris_surface_to_vol_distances.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SURFACE_TO_VOL_DISTANCES_METADATA = Metadata(
-    id="0803f1be3d6e6b156373a996f30cbdf91c784084.boutiques",
+    id="fafba889762effb030273d18df3d68b319b3f6a6.boutiques",
     name="mris_surface_to_vol_distances",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_SURFACE_TO_VOL_DISTANCES_METADATA = Metadata(
 
 
 MrisSurfaceToVolDistancesParameters = typing.TypedDict('MrisSurfaceToVolDistancesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_surface_to_vol_distances"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_surface_to_vol_distances"]],
+    "average_subject": str,
+    "hemisphere": str,
+    "subjects": list[str],
+    "output_prefix": str,
+})
+MrisSurfaceToVolDistancesParametersTagged = typing.TypedDict('MrisSurfaceToVolDistancesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_surface_to_vol_distances"],
     "average_subject": str,
     "hemisphere": str,
     "subjects": list[str],
     "output_prefix": 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_surface_to_vol_distances": mris_surface_to_vol_distances_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_surface_to_vol_distances": mris_surface_to_vol_distances_outputs,
-    }.get(t)
 
 
 class MrisSurfaceToVolDistancesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_surface_to_vol_distances(...)`.
+    Output object returned when calling `MrisSurfaceToVolDistancesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_surface_to_vol_distances_params(
     hemisphere: str,
     subjects: list[str],
     output_prefix: str,
-) -> MrisSurfaceToVolDistancesParameters:
+) -> MrisSurfaceToVolDistancesParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mris_surface_to_vol_distances_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_surface_to_vol_distances",
+        "@type": "freesurfer/mris_surface_to_vol_distances",
         "average_subject": average_subject,
         "hemisphere": hemisphere,
         "subjects": subjects,
@@ -106,10 +81,10 @@ def mris_surface_to_vol_distances_cargs(
     """
     cargs = []
     cargs.append("mris_surface_to_vol_distances")
-    cargs.append(params.get("average_subject"))
-    cargs.append(params.get("hemisphere"))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_prefix"))
+    cargs.append(params.get("average_subject", None))
+    cargs.append(params.get("hemisphere", None))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_prefix", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def mris_surface_to_vol_distances_outputs(
     """
     ret = MrisSurfaceToVolDistancesOutputs(
         root=execution.output_file("."),
-        output_distances=execution.output_file(params.get("output_prefix") + "_distances.txt"),
+        output_distances=execution.output_file(params.get("output_prefix", None) + "_distances.txt"),
     )
     return ret
 
 
 def mris_surface_to_vol_distances_execute(
     params: MrisSurfaceToVolDistancesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSurfaceToVolDistancesOutputs:
     """
+    mris_surface_to_vol_distances
+    
     Tool from FreeSurfer to calculate surface-to-volume distances.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def mris_surface_to_vol_distances_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSurfaceToVolDistancesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SURFACE_TO_VOL_DISTANCES_METADATA)
     params = execution.params(params)
     cargs = mris_surface_to_vol_distances_cargs(params, execution)
     ret = mris_surface_to_vol_distances_outputs(params, execution)
@@ -165,6 +144,8 @@ def mris_surface_to_vol_distances(
     runner: Runner | None = None,
 ) -> MrisSurfaceToVolDistancesOutputs:
     """
+    mris_surface_to_vol_distances
+    
     Tool from FreeSurfer to calculate surface-to-volume distances.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def mris_surface_to_vol_distances(
     Returns:
         NamedTuple of outputs (described in `MrisSurfaceToVolDistancesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SURFACE_TO_VOL_DISTANCES_METADATA)
     params = mris_surface_to_vol_distances_params(
         average_subject=average_subject,
         hemisphere=hemisphere,
         subjects=subjects,
         output_prefix=output_prefix,
     )
-    return mris_surface_to_vol_distances_execute(params, execution)
+    return mris_surface_to_vol_distances_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SURFACE_TO_VOL_DISTANCES_METADATA",
     "MrisSurfaceToVolDistancesOutputs",
-    "MrisSurfaceToVolDistancesParameters",
     "mris_surface_to_vol_distances",
+    "mris_surface_to_vol_distances_execute",
     "mris_surface_to_vol_distances_params",
 ]

niwrap_freesurfer/freesurfer/mris_talairach.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_TALAIRACH_METADATA = Metadata(
-    id="2a27ec50232d56f8e8e079035c459f747d644292.boutiques",
+    id="b14b564d4aba1a165b4b4ad9a8b05de7a0aabc95.boutiques",
     name="mris_talairach",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MRIS_TALAIRACH_METADATA = Metadata(
 
 
 MrisTalairachParameters = typing.TypedDict('MrisTalairachParameters', {
-    "__STYXTYPE__": typing.Literal["mris_talairach"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_talairach"]],
+    "input_image": InputPathType,
+})
+MrisTalairachParametersTagged = typing.TypedDict('MrisTalairachParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_talairach"],
     "input_image": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_talairach": mris_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 {
-    }.get(t)
 
 
 class MrisTalairachOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_talairach(...)`.
+    Output object returned when calling `MrisTalairachParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MrisTalairachOutputs(typing.NamedTuple):
 
 def mris_talairach_params(
     input_image: InputPathType,
-) -> MrisTalairachParameters:
+) -> MrisTalairachParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def mris_talairach_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_talairach",
+        "@type": "freesurfer/mris_talairach",
         "input_image": input_image,
     }
     return params
@@ -91,7 +64,7 @@ def mris_talairach_cargs(
     """
     cargs = []
     cargs.append("mris_talairach")
-    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(execution.input_file(params.get("input_image", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def mris_talairach_outputs(
 
 def mris_talairach_execute(
     params: MrisTalairachParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisTalairachOutputs:
     """
+    mris_talairach
+    
     Transforms an MRI surface into Talairach space.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def mris_talairach_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisTalairachOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_TALAIRACH_METADATA)
     params = execution.params(params)
     cargs = mris_talairach_cargs(params, execution)
     ret = mris_talairach_outputs(params, execution)
@@ -143,6 +120,8 @@ def mris_talairach(
     runner: Runner | None = None,
 ) -> MrisTalairachOutputs:
     """
+    mris_talairach
+    
     Transforms an MRI surface into Talairach space.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def mris_talairach(
     Returns:
         NamedTuple of outputs (described in `MrisTalairachOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_TALAIRACH_METADATA)
     params = mris_talairach_params(
         input_image=input_image,
     )
-    return mris_talairach_execute(params, execution)
+    return mris_talairach_execute(params, runner)
 
 
 __all__ = [
     "MRIS_TALAIRACH_METADATA",
     "MrisTalairachOutputs",
-    "MrisTalairachParameters",
     "mris_talairach",
+    "mris_talairach_execute",
     "mris_talairach_params",
 ]

niwrap_freesurfer/freesurfer/mris_target_pos.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_TARGET_POS_METADATA = Metadata(
-    id="80d94d231c04dec8bb4f30da7ea7a8bb0e15c938.boutiques",
+    id="a7ad1c96ec12bbd6703e8e4bb8235b624da111f1.boutiques",
     name="mris_target_pos",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ MRIS_TARGET_POS_METADATA = Metadata(
 
 
 MrisTargetPosParameters = typing.TypedDict('MrisTargetPosParameters', {
-    "__STYXTYPE__": typing.Literal["mris_target_pos"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_target_pos"]],
+    "input_volume": InputPathType,
+    "input_surface": InputPathType,
+    "output_surface": str,
+    "adgws_file": str,
+    "threshold_values": typing.NotRequired[list[float] | None],
+    "label": typing.NotRequired[str | None],
+    "interpolation_method": typing.NotRequired[str | None],
+    "debug_vertex": typing.NotRequired[float | None],
+    "cbv_flag": bool,
+    "debug_flag": bool,
+    "check_options": bool,
+    "help_flag": bool,
+    "version_flag": bool,
+})
+MrisTargetPosParametersTagged = typing.TypedDict('MrisTargetPosParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_target_pos"],
     "input_volume": InputPathType,
     "input_surface": InputPathType,
     "output_surface": str,
@@ -29,42 +45,11 @@ MrisTargetPosParameters = typing.TypedDict('MrisTargetPosParameters', {
     "help_flag": bool,
     "version_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_target_pos": mris_target_pos_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 MrisTargetPosOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_target_pos(...)`.
+    Output object returned when calling `MrisTargetPosParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def mris_target_pos_params(
     check_options: bool = False,
     help_flag: bool = False,
     version_flag: bool = False,
-) -> MrisTargetPosParameters:
+) -> MrisTargetPosParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +92,7 @@ def mris_target_pos_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_target_pos",
+        "@type": "freesurfer/mris_target_pos",
         "input_volume": input_volume,
         "input_surface": input_surface,
         "output_surface": output_surface,
@@ -146,49 +131,49 @@ def mris_target_pos_cargs(
     cargs.append("mris_target_pos")
     cargs.extend([
         "--v",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_surface"))
+        execution.input_file(params.get("input_surface", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_surface")
+        params.get("output_surface", None)
     ])
     cargs.extend([
         "--adgws",
-        params.get("adgws_file")
+        params.get("adgws_file", None)
     ])
-    if params.get("threshold_values") is not None:
+    if params.get("threshold_values", None) is not None:
         cargs.extend([
             "--thresh",
-            *map(str, params.get("threshold_values"))
+            *map(str, params.get("threshold_values", None))
         ])
-    if params.get("label") is not None:
+    if params.get("label", None) is not None:
         cargs.extend([
             "--l",
-            params.get("label")
+            params.get("label", None)
         ])
-    if params.get("interpolation_method") is not None:
+    if params.get("interpolation_method", None) is not None:
         cargs.extend([
             "--interp",
-            params.get("interpolation_method")
+            params.get("interpolation_method", None)
         ])
-    if params.get("debug_vertex") is not None:
+    if params.get("debug_vertex", None) is not None:
         cargs.extend([
             "--debug-vertex",
-            str(params.get("debug_vertex"))
+            str(params.get("debug_vertex", None))
         ])
-    if params.get("cbv_flag"):
+    if params.get("cbv_flag", False):
         cargs.append("--cbv")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("check_options"):
+    if params.get("check_options", False):
         cargs.append("--checkopts")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
     return cargs
 
@@ -214,9 +199,11 @@ def mris_target_pos_outputs(
 
 def mris_target_pos_execute(
     params: MrisTargetPosParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisTargetPosOutputs:
     """
+    mris_target_pos
+    
     Tool for setting target positions of a surface using input imaging data and
     other parameters.
     
@@ -226,10 +213,12 @@ def mris_target_pos_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisTargetPosOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_TARGET_POS_METADATA)
     params = execution.params(params)
     cargs = mris_target_pos_cargs(params, execution)
     ret = mris_target_pos_outputs(params, execution)
@@ -254,6 +243,8 @@ def mris_target_pos(
     runner: Runner | None = None,
 ) -> MrisTargetPosOutputs:
     """
+    mris_target_pos
+    
     Tool for setting target positions of a surface using input imaging data and
     other parameters.
     
@@ -280,8 +271,6 @@ def mris_target_pos(
     Returns:
         NamedTuple of outputs (described in `MrisTargetPosOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_TARGET_POS_METADATA)
     params = mris_target_pos_params(
         input_volume=input_volume,
         input_surface=input_surface,
@@ -297,13 +286,13 @@ def mris_target_pos(
         help_flag=help_flag,
         version_flag=version_flag,
     )
-    return mris_target_pos_execute(params, execution)
+    return mris_target_pos_execute(params, runner)
 
 
 __all__ = [
     "MRIS_TARGET_POS_METADATA",
     "MrisTargetPosOutputs",
-    "MrisTargetPosParameters",
     "mris_target_pos",
+    "mris_target_pos_execute",
     "mris_target_pos_params",
 ]