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

niwrap_freesurfer/freesurfer/fsl_5_0_2_xyztrans_sch.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSL_5_0_2_XYZTRANS_SCH_METADATA = Metadata(
-    id="2e8e3863e13fefc751213519c3123968f897e3e2.boutiques",
+    id="a3ebfe38f72e8d10f1cafe04c5df2e3fc2159be7.boutiques",
     name="fsl.5.0.2.xyztrans.sch",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ FSL_5_0_2_XYZTRANS_SCH_METADATA = Metadata(
 
 
 Fsl502XyztransSchParameters = typing.TypedDict('Fsl502XyztransSchParameters', {
-    "__STYXTYPE__": typing.Literal["fsl.5.0.2.xyztrans.sch"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsl.5.0.2.xyztrans.sch"]],
+    "term_option": typing.NotRequired[str | None],
+    "version_flag": bool,
+    "no_scrollback_flag": bool,
+})
+Fsl502XyztransSchParametersTagged = typing.TypedDict('Fsl502XyztransSchParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsl.5.0.2.xyztrans.sch"],
     "term_option": typing.NotRequired[str | None],
     "version_flag": bool,
     "no_scrollback_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 {
-        "fsl.5.0.2.xyztrans.sch": fsl_5_0_2_xyztrans_sch_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 Fsl502XyztransSchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsl_5_0_2_xyztrans_sch(...)`.
+    Output object returned when calling `Fsl502XyztransSchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def fsl_5_0_2_xyztrans_sch_params(
     term_option: str | None = None,
     version_flag: bool = False,
     no_scrollback_flag: bool = False,
-) -> Fsl502XyztransSchParameters:
+) -> Fsl502XyztransSchParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def fsl_5_0_2_xyztrans_sch_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsl.5.0.2.xyztrans.sch",
+        "@type": "freesurfer/fsl.5.0.2.xyztrans.sch",
         "version_flag": version_flag,
         "no_scrollback_flag": no_scrollback_flag,
     }
@@ -100,14 +75,14 @@ def fsl_5_0_2_xyztrans_sch_cargs(
     """
     cargs = []
     cargs.append("fsl.5.0.2.xyztrans.sch")
-    if params.get("term_option") is not None:
+    if params.get("term_option", None) is not None:
         cargs.extend([
             "-T",
-            params.get("term_option")
+            params.get("term_option", None)
         ])
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("-V")
-    if params.get("no_scrollback_flag"):
+    if params.get("no_scrollback_flag", False):
         cargs.append("-x")
     return cargs
 
@@ -133,10 +108,13 @@ def fsl_5_0_2_xyztrans_sch_outputs(
 
 def fsl_5_0_2_xyztrans_sch_execute(
     params: Fsl502XyztransSchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fsl502XyztransSchOutputs:
     """
-    A script with unclear functionality, potentially related to terminal operations.
+    fsl.5.0.2.xyztrans.sch
+    
+    A script with unclear functionality, potentially related to terminal
+    operations.
     
     Author: FreeSurfer Developers
     
@@ -144,10 +122,12 @@ def fsl_5_0_2_xyztrans_sch_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fsl502XyztransSchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSL_5_0_2_XYZTRANS_SCH_METADATA)
     params = execution.params(params)
     cargs = fsl_5_0_2_xyztrans_sch_cargs(params, execution)
     ret = fsl_5_0_2_xyztrans_sch_outputs(params, execution)
@@ -162,7 +142,10 @@ def fsl_5_0_2_xyztrans_sch(
     runner: Runner | None = None,
 ) -> Fsl502XyztransSchOutputs:
     """
-    A script with unclear functionality, potentially related to terminal operations.
+    fsl.5.0.2.xyztrans.sch
+    
+    A script with unclear functionality, potentially related to terminal
+    operations.
     
     Author: FreeSurfer Developers
     
@@ -176,20 +159,18 @@ def fsl_5_0_2_xyztrans_sch(
     Returns:
         NamedTuple of outputs (described in `Fsl502XyztransSchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSL_5_0_2_XYZTRANS_SCH_METADATA)
     params = fsl_5_0_2_xyztrans_sch_params(
         term_option=term_option,
         version_flag=version_flag,
         no_scrollback_flag=no_scrollback_flag,
     )
-    return fsl_5_0_2_xyztrans_sch_execute(params, execution)
+    return fsl_5_0_2_xyztrans_sch_execute(params, runner)
 
 
 __all__ = [
     "FSL_5_0_2_XYZTRANS_SCH_METADATA",
     "Fsl502XyztransSchOutputs",
-    "Fsl502XyztransSchParameters",
     "fsl_5_0_2_xyztrans_sch",
+    "fsl_5_0_2_xyztrans_sch_execute",
     "fsl_5_0_2_xyztrans_sch_params",
 ]

niwrap_freesurfer/freesurfer/fsl_label2voxel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSL_LABEL2VOXEL_METADATA = Metadata(
-    id="488fd9f6f8cf1cc2dafb238be876366f78aac9b2.boutiques",
+    id="b7cfa174c1d53b421fb427ab1a24c20eebcc6c94.boutiques",
     name="fsl_label2voxel",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ FSL_LABEL2VOXEL_METADATA = Metadata(
 
 
 FslLabel2voxelParameters = typing.TypedDict('FslLabel2voxelParameters', {
-    "__STYXTYPE__": typing.Literal["fsl_label2voxel"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsl_label2voxel"]],
+    "label_value": float,
+    "labeled_volume": InputPathType,
+    "src_volume": InputPathType,
+    "output_filename": str,
+})
+FslLabel2voxelParametersTagged = typing.TypedDict('FslLabel2voxelParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsl_label2voxel"],
     "label_value": float,
     "labeled_volume": InputPathType,
     "src_volume": InputPathType,
     "output_filename": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsl_label2voxel": fsl_label2voxel_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 {
-        "fsl_label2voxel": fsl_label2voxel_outputs,
-    }.get(t)
 
 
 class FslLabel2voxelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsl_label2voxel(...)`.
+    Output object returned when calling `FslLabel2voxelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def fsl_label2voxel_params(
     labeled_volume: InputPathType,
     src_volume: InputPathType,
     output_filename: str,
-) -> FslLabel2voxelParameters:
+) -> FslLabel2voxelParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def fsl_label2voxel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsl_label2voxel",
+        "@type": "freesurfer/fsl_label2voxel",
         "label_value": label_value,
         "labeled_volume": labeled_volume,
         "src_volume": src_volume,
@@ -106,10 +81,10 @@ def fsl_label2voxel_cargs(
     """
     cargs = []
     cargs.append("fsl_label2voxel")
-    cargs.append(str(params.get("label_value")))
-    cargs.append(execution.input_file(params.get("labeled_volume")))
-    cargs.append(execution.input_file(params.get("src_volume")))
-    cargs.append(params.get("output_filename"))
+    cargs.append(str(params.get("label_value", None)))
+    cargs.append(execution.input_file(params.get("labeled_volume", None)))
+    cargs.append(execution.input_file(params.get("src_volume", None)))
+    cargs.append(params.get("output_filename", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def fsl_label2voxel_outputs(
     """
     ret = FslLabel2voxelOutputs(
         root=execution.output_file("."),
-        output_voxel_data=execution.output_file(params.get("output_filename")),
+        output_voxel_data=execution.output_file(params.get("output_filename", None)),
     )
     return ret
 
 
 def fsl_label2voxel_execute(
     params: FslLabel2voxelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FslLabel2voxelOutputs:
     """
+    fsl_label2voxel
+    
     Converts labeled volumes to voxels based on specified labels.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def fsl_label2voxel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FslLabel2voxelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSL_LABEL2VOXEL_METADATA)
     params = execution.params(params)
     cargs = fsl_label2voxel_cargs(params, execution)
     ret = fsl_label2voxel_outputs(params, execution)
@@ -165,6 +144,8 @@ def fsl_label2voxel(
     runner: Runner | None = None,
 ) -> FslLabel2voxelOutputs:
     """
+    fsl_label2voxel
+    
     Converts labeled volumes to voxels based on specified labels.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def fsl_label2voxel(
     Returns:
         NamedTuple of outputs (described in `FslLabel2voxelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSL_LABEL2VOXEL_METADATA)
     params = fsl_label2voxel_params(
         label_value=label_value,
         labeled_volume=labeled_volume,
         src_volume=src_volume,
         output_filename=output_filename,
     )
-    return fsl_label2voxel_execute(params, execution)
+    return fsl_label2voxel_execute(params, runner)
 
 
 __all__ = [
     "FSL_LABEL2VOXEL_METADATA",
     "FslLabel2voxelOutputs",
-    "FslLabel2voxelParameters",
     "fsl_label2voxel",
+    "fsl_label2voxel_execute",
     "fsl_label2voxel_params",
 ]

niwrap_freesurfer/freesurfer/fsl_rigid_register.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSL_RIGID_REGISTER_METADATA = Metadata(
-    id="0e36527961ef5f32edd4250263430f3e00b08730.boutiques",
+    id="abd62e6795a7fb22e18676b3f84f7431ec93f8c9.boutiques",
     name="fsl_rigid_register",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,32 @@ FSL_RIGID_REGISTER_METADATA = Metadata(
 
 
 FslRigidRegisterParameters = typing.TypedDict('FslRigidRegisterParameters', {
-    "__STYXTYPE__": typing.Literal["fsl_rigid_register"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsl_rigid_register"]],
+    "refvol": InputPathType,
+    "inputvol": InputPathType,
+    "outputvol": str,
+    "fslmat": typing.NotRequired[str | None],
+    "regmat": typing.NotRequired[str | None],
+    "xfmmat": typing.NotRequired[str | None],
+    "ltamat": typing.NotRequired[str | None],
+    "noinitgeom": bool,
+    "applyxfm": typing.NotRequired[InputPathType | None],
+    "applyinitxfm": bool,
+    "initxfm": typing.NotRequired[InputPathType | None],
+    "maxangle": typing.NotRequired[float | None],
+    "interp": typing.NotRequired[str | None],
+    "dof": typing.NotRequired[float | None],
+    "bins": typing.NotRequired[float | None],
+    "cost": typing.NotRequired[str | None],
+    "tmpdir": typing.NotRequired[str | None],
+    "nocleanup": bool,
+    "cleanup": bool,
+    "subject": typing.NotRequired[str | None],
+    "version": bool,
+    "help": bool,
+})
+FslRigidRegisterParametersTagged = typing.TypedDict('FslRigidRegisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsl_rigid_register"],
     "refvol": InputPathType,
     "inputvol": InputPathType,
     "outputvol": str,
@@ -38,43 +63,11 @@ FslRigidRegisterParameters = typing.TypedDict('FslRigidRegisterParameters', {
     "version": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsl_rigid_register": fsl_rigid_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 {
-        "fsl_rigid_register": fsl_rigid_register_outputs,
-    }.get(t)
 
 
 class FslRigidRegisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsl_rigid_register(...)`.
+    Output object returned when calling `FslRigidRegisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -105,7 +98,7 @@ def fsl_rigid_register_params(
     subject: str | None = None,
     version: bool = False,
     help_: bool = False,
-) -> FslRigidRegisterParameters:
+) -> FslRigidRegisterParametersTagged:
     """
     Build parameters.
     
@@ -140,7 +133,7 @@ def fsl_rigid_register_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsl_rigid_register",
+        "@type": "freesurfer/fsl_rigid_register",
         "refvol": refvol,
         "inputvol": inputvol,
         "outputvol": outputvol,
@@ -197,92 +190,92 @@ def fsl_rigid_register_cargs(
     cargs.append("fsl_rigid_register")
     cargs.extend([
         "-r",
-        execution.input_file(params.get("refvol"))
+        execution.input_file(params.get("refvol", None))
     ])
     cargs.extend([
         "-i",
-        execution.input_file(params.get("inputvol"))
+        execution.input_file(params.get("inputvol", None))
     ])
     cargs.extend([
         "-o",
-        params.get("outputvol")
+        params.get("outputvol", None)
     ])
-    if params.get("fslmat") is not None:
+    if params.get("fslmat", None) is not None:
         cargs.extend([
             "-fslmat",
-            params.get("fslmat")
+            params.get("fslmat", None)
         ])
-    if params.get("regmat") is not None:
+    if params.get("regmat", None) is not None:
         cargs.extend([
             "-regmat",
-            params.get("regmat")
+            params.get("regmat", None)
         ])
-    if params.get("xfmmat") is not None:
+    if params.get("xfmmat", None) is not None:
         cargs.extend([
             "-xfmmat",
-            params.get("xfmmat")
+            params.get("xfmmat", None)
         ])
-    if params.get("ltamat") is not None:
+    if params.get("ltamat", None) is not None:
         cargs.extend([
             "-ltamat",
-            params.get("ltamat")
+            params.get("ltamat", None)
         ])
-    if params.get("noinitgeom"):
+    if params.get("noinitgeom", False):
         cargs.append("-noinitgeom")
-    if params.get("applyxfm") is not None:
+    if params.get("applyxfm", None) is not None:
         cargs.extend([
             "-applyxfm",
-            execution.input_file(params.get("applyxfm"))
+            execution.input_file(params.get("applyxfm", None))
         ])
-    if params.get("applyinitxfm"):
+    if params.get("applyinitxfm", False):
         cargs.append("-applyinitxfm")
-    if params.get("initxfm") is not None:
+    if params.get("initxfm", None) is not None:
         cargs.extend([
             "-initxfm",
-            execution.input_file(params.get("initxfm"))
+            execution.input_file(params.get("initxfm", None))
         ])
-    if params.get("maxangle") is not None:
+    if params.get("maxangle", None) is not None:
         cargs.extend([
             "-maxangle",
-            str(params.get("maxangle"))
+            str(params.get("maxangle", None))
         ])
-    if params.get("interp") is not None:
+    if params.get("interp", None) is not None:
         cargs.extend([
             "-interp",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("dof") is not None:
+    if params.get("dof", None) is not None:
         cargs.extend([
             "-dof",
-            str(params.get("dof"))
+            str(params.get("dof", None))
         ])
-    if params.get("bins") is not None:
+    if params.get("bins", None) is not None:
         cargs.extend([
             "-bins",
-            str(params.get("bins"))
+            str(params.get("bins", None))
         ])
-    if params.get("cost") is not None:
+    if params.get("cost", None) is not None:
         cargs.extend([
             "-cost",
-            params.get("cost")
+            params.get("cost", None)
         ])
-    if params.get("tmpdir") is not None:
+    if params.get("tmpdir", None) is not None:
         cargs.extend([
             "-tmpdir",
-            params.get("tmpdir")
+            params.get("tmpdir", None)
         ])
-    if params.get("nocleanup"):
+    if params.get("nocleanup", False):
         cargs.append("-nocleanup")
-    if params.get("cleanup"):
+    if params.get("cleanup", False):
         cargs.append("-cleanup")
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "-subject",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -302,18 +295,20 @@ def fsl_rigid_register_outputs(
     """
     ret = FslRigidRegisterOutputs(
         root=execution.output_file("."),
-        fslmat_output=execution.output_file(params.get("outputvol") + ".fslmat"),
+        fslmat_output=execution.output_file(params.get("outputvol", None) + ".fslmat"),
     )
     return ret
 
 
 def fsl_rigid_register_execute(
     params: FslRigidRegisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FslRigidRegisterOutputs:
     """
-    A front-end tool for FSL's FLIRT that computes a rigid registration matrix and
-    resamples the input volume to the reference volume.
+    fsl_rigid_register
+    
+    A front-end tool for FSL's FLIRT that computes a rigid registration matrix
+    and resamples the input volume to the reference volume.
     
     Author: FreeSurfer Developers
     
@@ -321,10 +316,12 @@ def fsl_rigid_register_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FslRigidRegisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSL_RIGID_REGISTER_METADATA)
     params = execution.params(params)
     cargs = fsl_rigid_register_cargs(params, execution)
     ret = fsl_rigid_register_outputs(params, execution)
@@ -358,8 +355,10 @@ def fsl_rigid_register(
     runner: Runner | None = None,
 ) -> FslRigidRegisterOutputs:
     """
-    A front-end tool for FSL's FLIRT that computes a rigid registration matrix and
-    resamples the input volume to the reference volume.
+    fsl_rigid_register
+    
+    A front-end tool for FSL's FLIRT that computes a rigid registration matrix
+    and resamples the input volume to the reference volume.
     
     Author: FreeSurfer Developers
     
@@ -396,8 +395,6 @@ def fsl_rigid_register(
     Returns:
         NamedTuple of outputs (described in `FslRigidRegisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSL_RIGID_REGISTER_METADATA)
     params = fsl_rigid_register_params(
         refvol=refvol,
         inputvol=inputvol,
@@ -422,13 +419,13 @@ def fsl_rigid_register(
         version=version,
         help_=help_,
     )
-    return fsl_rigid_register_execute(params, execution)
+    return fsl_rigid_register_execute(params, runner)
 
 
 __all__ = [
     "FSL_RIGID_REGISTER_METADATA",
     "FslRigidRegisterOutputs",
-    "FslRigidRegisterParameters",
     "fsl_rigid_register",
+    "fsl_rigid_register_execute",
     "fsl_rigid_register_params",
 ]