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

niwrap_freesurfer/freesurfer/avi2talxfm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AVI2TALXFM_METADATA = Metadata(
-    id="dd49fcac45ac0aee8f33fc3c39f2335f058798ac.boutiques",
+    id="b2655b0f30995a088bcf42b9c6db2e6477fd8f33.boutiques",
     name="avi2talxfm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ AVI2TALXFM_METADATA = Metadata(
 
 
 Avi2talxfmParameters = typing.TypedDict('Avi2talxfmParameters', {
-    "__STYXTYPE__": typing.Literal["avi2talxfm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/avi2talxfm"]],
+    "input_volume": InputPathType,
+    "target_volume": InputPathType,
+    "vox2vox_transform": InputPathType,
+    "output_xfm": str,
+})
+Avi2talxfmParametersTagged = typing.TypedDict('Avi2talxfmParametersTagged', {
+    "@type": typing.Literal["freesurfer/avi2talxfm"],
     "input_volume": InputPathType,
     "target_volume": InputPathType,
     "vox2vox_transform": InputPathType,
     "output_xfm": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "avi2talxfm": avi2talxfm_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 {
-        "avi2talxfm": avi2talxfm_outputs,
-    }.get(t)
 
 
 class Avi2talxfmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `avi2talxfm(...)`.
+    Output object returned when calling `Avi2talxfmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def avi2talxfm_params(
     target_volume: InputPathType,
     vox2vox_transform: InputPathType,
     output_xfm: str,
-) -> Avi2talxfmParameters:
+) -> Avi2talxfmParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def avi2talxfm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "avi2talxfm",
+        "@type": "freesurfer/avi2talxfm",
         "input_volume": input_volume,
         "target_volume": target_volume,
         "vox2vox_transform": vox2vox_transform,
@@ -106,10 +81,10 @@ def avi2talxfm_cargs(
     """
     cargs = []
     cargs.append("avi2talxfm")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("target_volume")))
-    cargs.append(execution.input_file(params.get("vox2vox_transform")))
-    cargs.append(params.get("output_xfm"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("target_volume", None)))
+    cargs.append(execution.input_file(params.get("vox2vox_transform", None)))
+    cargs.append(params.get("output_xfm", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def avi2talxfm_outputs(
     """
     ret = Avi2talxfmOutputs(
         root=execution.output_file("."),
-        output_xfm_file=execution.output_file(params.get("output_xfm")),
+        output_xfm_file=execution.output_file(params.get("output_xfm", None)),
     )
     return ret
 
 
 def avi2talxfm_execute(
     params: Avi2talxfmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Avi2talxfmOutputs:
     """
+    avi2talxfm
+    
     Convert voxel-to-voxel transform to MNI transform.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def avi2talxfm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Avi2talxfmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AVI2TALXFM_METADATA)
     params = execution.params(params)
     cargs = avi2talxfm_cargs(params, execution)
     ret = avi2talxfm_outputs(params, execution)
@@ -165,6 +144,8 @@ def avi2talxfm(
     runner: Runner | None = None,
 ) -> Avi2talxfmOutputs:
     """
+    avi2talxfm
+    
     Convert voxel-to-voxel transform to MNI transform.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def avi2talxfm(
     Returns:
         NamedTuple of outputs (described in `Avi2talxfmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AVI2TALXFM_METADATA)
     params = avi2talxfm_params(
         input_volume=input_volume,
         target_volume=target_volume,
         vox2vox_transform=vox2vox_transform,
         output_xfm=output_xfm,
     )
-    return avi2talxfm_execute(params, execution)
+    return avi2talxfm_execute(params, runner)
 
 
 __all__ = [
     "AVI2TALXFM_METADATA",
     "Avi2talxfmOutputs",
-    "Avi2talxfmParameters",
     "avi2talxfm",
+    "avi2talxfm_execute",
     "avi2talxfm_params",
 ]

niwrap_freesurfer/freesurfer/bblabel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BBLABEL_METADATA = Metadata(
-    id="d1293820501628cd990eec4b275ecca954c2d046.boutiques",
+    id="d69daa37c1949c73cb1a095891176caf6eaff2ee.boutiques",
     name="bblabel",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ BBLABEL_METADATA = Metadata(
 
 
 BblabelParameters = typing.TypedDict('BblabelParameters', {
-    "__STYXTYPE__": typing.Literal["bblabel"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/bblabel"]],
+    "labelfile": InputPathType,
+    "xmin": typing.NotRequired[float | None],
+    "xmax": typing.NotRequired[float | None],
+    "ymin": typing.NotRequired[float | None],
+    "ymax": typing.NotRequired[float | None],
+    "zmin": typing.NotRequired[float | None],
+    "zmax": typing.NotRequired[float | None],
+    "outlabelfile": str,
+    "debug": bool,
+    "umask": typing.NotRequired[str | None],
+})
+BblabelParametersTagged = typing.TypedDict('BblabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/bblabel"],
     "labelfile": InputPathType,
     "xmin": typing.NotRequired[float | None],
     "xmax": typing.NotRequired[float | None],
@@ -26,43 +39,11 @@ BblabelParameters = typing.TypedDict('BblabelParameters', {
     "debug": bool,
     "umask": 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 {
-        "bblabel": bblabel_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 {
-        "bblabel": bblabel_outputs,
-    }.get(t)
 
 
 class BblabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bblabel(...)`.
+    Output object returned when calling `BblabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def bblabel_params(
     zmax: float | None = None,
     debug: bool = False,
     umask: str | None = None,
-) -> BblabelParameters:
+) -> BblabelParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +81,7 @@ def bblabel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bblabel",
+        "@type": "freesurfer/bblabel",
         "labelfile": labelfile,
         "outlabelfile": outlabelfile,
         "debug": debug,
@@ -139,48 +120,48 @@ def bblabel_cargs(
     cargs.append("bblabel")
     cargs.extend([
         "--l",
-        execution.input_file(params.get("labelfile"))
+        execution.input_file(params.get("labelfile", None))
     ])
-    if params.get("xmin") is not None:
+    if params.get("xmin", None) is not None:
         cargs.extend([
             "--xmin",
-            str(params.get("xmin"))
+            str(params.get("xmin", None))
         ])
-    if params.get("xmax") is not None:
+    if params.get("xmax", None) is not None:
         cargs.extend([
             "--xmax",
-            str(params.get("xmax"))
+            str(params.get("xmax", None))
         ])
-    if params.get("ymin") is not None:
+    if params.get("ymin", None) is not None:
         cargs.extend([
             "--ymin",
-            str(params.get("ymin"))
+            str(params.get("ymin", None))
         ])
-    if params.get("ymax") is not None:
+    if params.get("ymax", None) is not None:
         cargs.extend([
             "--ymax",
-            str(params.get("ymax"))
+            str(params.get("ymax", None))
         ])
-    if params.get("zmin") is not None:
+    if params.get("zmin", None) is not None:
         cargs.extend([
             "--zmin",
-            str(params.get("zmin"))
+            str(params.get("zmin", None))
         ])
-    if params.get("zmax") is not None:
+    if params.get("zmax", None) is not None:
         cargs.extend([
             "--zmax",
-            str(params.get("zmax"))
+            str(params.get("zmax", None))
         ])
     cargs.extend([
         "--o",
-        params.get("outlabelfile")
+        params.get("outlabelfile", None)
     ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "--umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
     return cargs
 
@@ -200,16 +181,18 @@ def bblabel_outputs(
     """
     ret = BblabelOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("outlabelfile")),
+        output_file=execution.output_file(params.get("outlabelfile", None)),
     )
     return ret
 
 
 def bblabel_execute(
     params: BblabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BblabelOutputs:
     """
+    bblabel
+    
     Applies a bounding box to a label, copying only the label points within the
     specified box to the output.
     
@@ -219,10 +202,12 @@ def bblabel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BblabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BBLABEL_METADATA)
     params = execution.params(params)
     cargs = bblabel_cargs(params, execution)
     ret = bblabel_outputs(params, execution)
@@ -244,6 +229,8 @@ def bblabel(
     runner: Runner | None = None,
 ) -> BblabelOutputs:
     """
+    bblabel
+    
     Applies a bounding box to a label, copying only the label points within the
     specified box to the output.
     
@@ -266,8 +253,6 @@ def bblabel(
     Returns:
         NamedTuple of outputs (described in `BblabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BBLABEL_METADATA)
     params = bblabel_params(
         labelfile=labelfile,
         xmin=xmin,
@@ -280,13 +265,13 @@ def bblabel(
         debug=debug,
         umask=umask,
     )
-    return bblabel_execute(params, execution)
+    return bblabel_execute(params, runner)
 
 
 __all__ = [
     "BBLABEL_METADATA",
     "BblabelOutputs",
-    "BblabelParameters",
     "bblabel",
+    "bblabel_execute",
     "bblabel_params",
 ]

niwrap_freesurfer/freesurfer/bbmask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BBMASK_METADATA = Metadata(
-    id="3655e677c7fb826f63ccb1bcc455303aa52c7b56.boutiques",
+    id="a836059c0ed308457e36032736d75953ebf2eb7e.boutiques",
     name="bbmask",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ BBMASK_METADATA = Metadata(
 
 
 BbmaskParameters = typing.TypedDict('BbmaskParameters', {
-    "__STYXTYPE__": typing.Literal["bbmask"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/bbmask"]],
+    "mask": list[InputPathType],
+    "src_volumes": typing.NotRequired[list[InputPathType] | None],
+    "npad": typing.NotRequired[float | None],
+    "registration": typing.NotRequired[list[InputPathType] | None],
+    "regheader": typing.NotRequired[InputPathType | None],
+    "sub2src": typing.NotRequired[InputPathType | None],
+})
+BbmaskParametersTagged = typing.TypedDict('BbmaskParametersTagged', {
+    "@type": typing.Literal["freesurfer/bbmask"],
     "mask": list[InputPathType],
     "src_volumes": typing.NotRequired[list[InputPathType] | None],
     "npad": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ BbmaskParameters = typing.TypedDict('BbmaskParameters', {
     "regheader": typing.NotRequired[InputPathType | None],
     "sub2src": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "bbmask": bbmask_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 {
-        "bbmask": bbmask_outputs,
-    }.get(t)
 
 
 class BbmaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bbmask(...)`.
+    Output object returned when calling `BbmaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +58,7 @@ def bbmask_params(
     registration: list[InputPathType] | None = None,
     regheader: InputPathType | None = None,
     sub2src: InputPathType | None = None,
-) -> BbmaskParameters:
+) -> BbmaskParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +74,7 @@ def bbmask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bbmask",
+        "@type": "freesurfer/bbmask",
         "mask": mask,
     }
     if src_volumes is not None:
@@ -130,32 +107,32 @@ def bbmask_cargs(
     cargs.append("bbmask")
     cargs.extend([
         "--mask",
-        *[execution.input_file(f) for f in params.get("mask")]
+        *[execution.input_file(f) for f in params.get("mask", None)]
     ])
-    if params.get("src_volumes") is not None:
+    if params.get("src_volumes", None) is not None:
         cargs.extend([
             "--src",
-            *[execution.input_file(f) for f in params.get("src_volumes")]
+            *[execution.input_file(f) for f in params.get("src_volumes", None)]
         ])
-    if params.get("npad") is not None:
+    if params.get("npad", None) is not None:
         cargs.extend([
             "--npad",
-            str(params.get("npad"))
+            str(params.get("npad", None))
         ])
-    if params.get("registration") is not None:
+    if params.get("registration", None) is not None:
         cargs.extend([
             "--reg",
-            *[execution.input_file(f) for f in params.get("registration")]
+            *[execution.input_file(f) for f in params.get("registration", None)]
         ])
-    if params.get("regheader") is not None:
+    if params.get("regheader", None) is not None:
         cargs.extend([
             "--regheader",
-            execution.input_file(params.get("regheader"))
+            execution.input_file(params.get("regheader", None))
         ])
-    if params.get("sub2src") is not None:
+    if params.get("sub2src", None) is not None:
         cargs.extend([
             "--sub2src",
-            execution.input_file(params.get("sub2src"))
+            execution.input_file(params.get("sub2src", None))
         ])
     return cargs
 
@@ -186,11 +163,13 @@ def bbmask_outputs(
 
 def bbmask_execute(
     params: BbmaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BbmaskOutputs:
     """
-    Tool to create a volume with a smaller field of view by creating a bounding box
-    that encompasses a mask.
+    bbmask
+    
+    Tool to create a volume with a smaller field of view by creating a bounding
+    box that encompasses a mask.
     
     Author: FreeSurfer Developers
     
@@ -198,10 +177,12 @@ def bbmask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BbmaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BBMASK_METADATA)
     params = execution.params(params)
     cargs = bbmask_cargs(params, execution)
     ret = bbmask_outputs(params, execution)
@@ -219,8 +200,10 @@ def bbmask(
     runner: Runner | None = None,
 ) -> BbmaskOutputs:
     """
-    Tool to create a volume with a smaller field of view by creating a bounding box
-    that encompasses a mask.
+    bbmask
+    
+    Tool to create a volume with a smaller field of view by creating a bounding
+    box that encompasses a mask.
     
     Author: FreeSurfer Developers
     
@@ -238,8 +221,6 @@ def bbmask(
     Returns:
         NamedTuple of outputs (described in `BbmaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BBMASK_METADATA)
     params = bbmask_params(
         mask=mask,
         src_volumes=src_volumes,
@@ -248,13 +229,13 @@ def bbmask(
         regheader=regheader,
         sub2src=sub2src,
     )
-    return bbmask_execute(params, execution)
+    return bbmask_execute(params, runner)
 
 
 __all__ = [
     "BBMASK_METADATA",
     "BbmaskOutputs",
-    "BbmaskParameters",
     "bbmask",
+    "bbmask_execute",
     "bbmask_params",
 ]