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

niwrap_freesurfer/freesurfer/make_symmetric.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_SYMMETRIC_METADATA = Metadata(
-    id="1c653a3729e019c1a68b0edb9c44bee8ba0b0c6c.boutiques",
+    id="f7911ae43f7d52c0040da49b8674456c4206f174.boutiques",
     name="make_symmetric",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MAKE_SYMMETRIC_METADATA = Metadata(
 
 
 MakeSymmetricParameters = typing.TypedDict('MakeSymmetricParameters', {
-    "__STYXTYPE__": typing.Literal["make_symmetric"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_symmetric"]],
+    "hemi": str,
+    "input_file": InputPathType,
+    "output_file": str,
+    "transform_map": str,
+})
+MakeSymmetricParametersTagged = typing.TypedDict('MakeSymmetricParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_symmetric"],
     "hemi": str,
     "input_file": InputPathType,
     "output_file": str,
     "transform_map": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make_symmetric": make_symmetric_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 {
-        "make_symmetric": make_symmetric_outputs,
-    }.get(t)
 
 
 class MakeSymmetricOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_symmetric(...)`.
+    Output object returned when calling `MakeSymmetricParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +46,7 @@ def make_symmetric_params(
     input_file: InputPathType,
     output_file: str,
     transform_map: str,
-) -> MakeSymmetricParameters:
+) -> MakeSymmetricParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +62,7 @@ def make_symmetric_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_symmetric",
+        "@type": "freesurfer/make_symmetric",
         "hemi": hemi,
         "input_file": input_file,
         "output_file": output_file,
@@ -111,10 +86,10 @@ def make_symmetric_cargs(
     """
     cargs = []
     cargs.append("make_symmetric")
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
-    cargs.append(params.get("transform_map"))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
+    cargs.append(params.get("transform_map", None))
     return cargs
 
 
@@ -133,17 +108,19 @@ def make_symmetric_outputs(
     """
     ret = MakeSymmetricOutputs(
         root=execution.output_file("."),
-        processed_output=execution.output_file(params.get("output_file")),
-        map_output=execution.output_file(params.get("transform_map")),
+        processed_output=execution.output_file(params.get("output_file", None)),
+        map_output=execution.output_file(params.get("transform_map", None)),
     )
     return ret
 
 
 def make_symmetric_execute(
     params: MakeSymmetricParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeSymmetricOutputs:
     """
+    make_symmetric
+    
     Registers an input image to its left/right reversed version using
     mri_robust_register in a half-way space and mirrors the selected hemisphere.
     
@@ -153,10 +130,12 @@ def make_symmetric_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeSymmetricOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_SYMMETRIC_METADATA)
     params = execution.params(params)
     cargs = make_symmetric_cargs(params, execution)
     ret = make_symmetric_outputs(params, execution)
@@ -172,6 +151,8 @@ def make_symmetric(
     runner: Runner | None = None,
 ) -> MakeSymmetricOutputs:
     """
+    make_symmetric
+    
     Registers an input image to its left/right reversed version using
     mri_robust_register in a half-way space and mirrors the selected hemisphere.
     
@@ -191,21 +172,19 @@ def make_symmetric(
     Returns:
         NamedTuple of outputs (described in `MakeSymmetricOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_SYMMETRIC_METADATA)
     params = make_symmetric_params(
         hemi=hemi,
         input_file=input_file,
         output_file=output_file,
         transform_map=transform_map,
     )
-    return make_symmetric_execute(params, execution)
+    return make_symmetric_execute(params, runner)
 
 
 __all__ = [
     "MAKE_SYMMETRIC_METADATA",
     "MakeSymmetricOutputs",
-    "MakeSymmetricParameters",
     "make_symmetric",
+    "make_symmetric_execute",
     "make_symmetric_params",
 ]

niwrap_freesurfer/freesurfer/make_upright.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_UPRIGHT_METADATA = Metadata(
-    id="9a8f85ef83b8eb4c40293a66c43256e0c3863123.boutiques",
+    id="a8076958c8c06cd60fb1da570c38bf38b5fe2a6d.boutiques",
     name="make_upright",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MAKE_UPRIGHT_METADATA = Metadata(
 
 
 MakeUprightParameters = typing.TypedDict('MakeUprightParameters', {
-    "__STYXTYPE__": typing.Literal["make_upright"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_upright"]],
+    "input_image": InputPathType,
+    "output_image": str,
+    "transformation_map": InputPathType,
+})
+MakeUprightParametersTagged = typing.TypedDict('MakeUprightParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_upright"],
     "input_image": InputPathType,
     "output_image": str,
     "transformation_map": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make_upright": make_upright_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 {
-        "make_upright": make_upright_outputs,
-    }.get(t)
 
 
 class MakeUprightOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_upright(...)`.
+    Output object returned when calling `MakeUprightParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def make_upright_params(
     input_image: InputPathType,
     output_image: str,
     transformation_map: InputPathType,
-) -> MakeUprightParameters:
+) -> MakeUprightParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def make_upright_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_upright",
+        "@type": "freesurfer/make_upright",
         "input_image": input_image,
         "output_image": output_image,
         "transformation_map": transformation_map,
@@ -102,9 +76,9 @@ def make_upright_cargs(
     """
     cargs = []
     cargs.append("make_upright")
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_image"))
-    cargs.append(execution.input_file(params.get("transformation_map")))
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(params.get("output_image", None))
+    cargs.append(execution.input_file(params.get("transformation_map", None)))
     return cargs
 
 
@@ -123,19 +97,21 @@ def make_upright_outputs(
     """
     ret = MakeUprightOutputs(
         root=execution.output_file("."),
-        registered_image=execution.output_file(params.get("output_image")),
+        registered_image=execution.output_file(params.get("output_image", None)),
     )
     return ret
 
 
 def make_upright_execute(
     params: MakeUprightParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeUprightOutputs:
     """
-    Registers MRI input to the left/right reversed version using mri_robust_register
-    and making use of the half-way space, resulting in an upright, forward facing
-    head position.
+    make_upright
+    
+    Registers MRI input to the left/right reversed version using
+    mri_robust_register and making use of the half-way space, resulting in an
+    upright, forward facing head position.
     
     Author: FreeSurfer Developers
     
@@ -143,10 +119,12 @@ def make_upright_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeUprightOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_UPRIGHT_METADATA)
     params = execution.params(params)
     cargs = make_upright_cargs(params, execution)
     ret = make_upright_outputs(params, execution)
@@ -161,9 +139,11 @@ def make_upright(
     runner: Runner | None = None,
 ) -> MakeUprightOutputs:
     """
-    Registers MRI input to the left/right reversed version using mri_robust_register
-    and making use of the half-way space, resulting in an upright, forward facing
-    head position.
+    make_upright
+    
+    Registers MRI input to the left/right reversed version using
+    mri_robust_register and making use of the half-way space, resulting in an
+    upright, forward facing head position.
     
     Author: FreeSurfer Developers
     
@@ -177,20 +157,18 @@ def make_upright(
     Returns:
         NamedTuple of outputs (described in `MakeUprightOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_UPRIGHT_METADATA)
     params = make_upright_params(
         input_image=input_image,
         output_image=output_image,
         transformation_map=transformation_map,
     )
-    return make_upright_execute(params, execution)
+    return make_upright_execute(params, runner)
 
 
 __all__ = [
     "MAKE_UPRIGHT_METADATA",
     "MakeUprightOutputs",
-    "MakeUprightParameters",
     "make_upright",
+    "make_upright_execute",
     "make_upright_params",
 ]

niwrap_freesurfer/freesurfer/makevol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKEVOL_METADATA = Metadata(
-    id="7ba1673b88b708e09827f8b5508b94dd83a88054.boutiques",
+    id="8802efdad5a767387b2e4e04a7189b59ea97e217.boutiques",
     name="makevol",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MAKEVOL_METADATA = Metadata(
 
 
 MakevolParameters = typing.TypedDict('MakevolParameters', {
-    "__STYXTYPE__": typing.Literal["makevol"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/makevol"]],
+    "filename": typing.NotRequired[str | None],
+    "width": typing.NotRequired[int | None],
+    "height": typing.NotRequired[int | None],
+    "depth": typing.NotRequired[int | None],
+    "sizex": typing.NotRequired[float | None],
+    "sizey": typing.NotRequired[float | None],
+    "sizez": typing.NotRequired[float | None],
+    "set_method": typing.NotRequired[str | None],
+})
+MakevolParametersTagged = typing.TypedDict('MakevolParametersTagged', {
+    "@type": typing.Literal["freesurfer/makevol"],
     "filename": typing.NotRequired[str | None],
     "width": typing.NotRequired[int | None],
     "height": typing.NotRequired[int | None],
@@ -24,43 +35,11 @@ MakevolParameters = typing.TypedDict('MakevolParameters', {
     "sizez": typing.NotRequired[float | None],
     "set_method": 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 {
-        "makevol": makevol_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 {
-        "makevol": makevol_outputs,
-    }.get(t)
 
 
 class MakevolOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `makevol(...)`.
+    Output object returned when calling `MakevolParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,15 +48,15 @@ class MakevolOutputs(typing.NamedTuple):
 
 
 def makevol_params(
-    filename: str | None = "new_volume.mgz",
-    width: int | None = 256,
-    height: int | None = 256,
-    depth: int | None = 256,
-    sizex: float | None = 1.0,
-    sizey: float | None = 1.0,
-    sizez: float | None = 1.0,
-    set_method: str | None = "xyz",
-) -> MakevolParameters:
+    filename: str | None = None,
+    width: int | None = None,
+    height: int | None = None,
+    depth: int | None = None,
+    sizex: float | None = None,
+    sizey: float | None = None,
+    sizez: float | None = None,
+    set_method: str | None = None,
+) -> MakevolParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def makevol_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "makevol",
+        "@type": "freesurfer/makevol",
     }
     if filename is not None:
         params["filename"] = filename
@@ -131,45 +110,45 @@ def makevol_cargs(
     """
     cargs = []
     cargs.append("makevol")
-    if params.get("filename") is not None:
+    if params.get("filename", None) is not None:
         cargs.extend([
             "-f",
-            params.get("filename")
+            params.get("filename", None)
         ])
-    if params.get("width") is not None:
+    if params.get("width", None) is not None:
         cargs.extend([
             "-x",
-            str(params.get("width"))
+            str(params.get("width", None))
         ])
-    if params.get("height") is not None:
+    if params.get("height", None) is not None:
         cargs.extend([
             "-y",
-            str(params.get("height"))
+            str(params.get("height", None))
         ])
-    if params.get("depth") is not None:
+    if params.get("depth", None) is not None:
         cargs.extend([
             "-z",
-            str(params.get("depth"))
+            str(params.get("depth", None))
         ])
-    if params.get("sizex") is not None:
+    if params.get("sizex", None) is not None:
         cargs.extend([
             "--sizex",
-            str(params.get("sizex"))
+            str(params.get("sizex", None))
         ])
-    if params.get("sizey") is not None:
+    if params.get("sizey", None) is not None:
         cargs.extend([
             "--sizey",
-            str(params.get("sizey"))
+            str(params.get("sizey", None))
         ])
-    if params.get("sizez") is not None:
+    if params.get("sizez", None) is not None:
         cargs.extend([
             "--sizez",
-            str(params.get("sizez"))
+            str(params.get("sizez", None))
         ])
-    if params.get("set_method") is not None:
+    if params.get("set_method", None) is not None:
         cargs.extend([
             "--set-method",
-            params.get("set_method")
+            params.get("set_method", None)
         ])
     return cargs
 
@@ -189,16 +168,18 @@ def makevol_outputs(
     """
     ret = MakevolOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("filename")) if (params.get("filename") is not None) else None,
+        output_file=execution.output_file(params.get("filename", None)) if (params.get("filename") is not None) else None,
     )
     return ret
 
 
 def makevol_execute(
     params: MakevolParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakevolOutputs:
     """
+    makevol
+    
     A tool to create a volume with given parameters.
     
     Author: FreeSurfer Developers
@@ -207,10 +188,12 @@ def makevol_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakevolOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKEVOL_METADATA)
     params = execution.params(params)
     cargs = makevol_cargs(params, execution)
     ret = makevol_outputs(params, execution)
@@ -219,17 +202,19 @@ def makevol_execute(
 
 
 def makevol(
-    filename: str | None = "new_volume.mgz",
-    width: int | None = 256,
-    height: int | None = 256,
-    depth: int | None = 256,
-    sizex: float | None = 1.0,
-    sizey: float | None = 1.0,
-    sizez: float | None = 1.0,
-    set_method: str | None = "xyz",
+    filename: str | None = None,
+    width: int | None = None,
+    height: int | None = None,
+    depth: int | None = None,
+    sizex: float | None = None,
+    sizey: float | None = None,
+    sizez: float | None = None,
+    set_method: str | None = None,
     runner: Runner | None = None,
 ) -> MakevolOutputs:
     """
+    makevol
+    
     A tool to create a volume with given parameters.
     
     Author: FreeSurfer Developers
@@ -250,8 +235,6 @@ def makevol(
     Returns:
         NamedTuple of outputs (described in `MakevolOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKEVOL_METADATA)
     params = makevol_params(
         filename=filename,
         width=width,
@@ -262,13 +245,13 @@ def makevol(
         sizez=sizez,
         set_method=set_method,
     )
-    return makevol_execute(params, execution)
+    return makevol_execute(params, runner)
 
 
 __all__ = [
     "MAKEVOL_METADATA",
     "MakevolOutputs",
-    "MakevolParameters",
     "makevol",
+    "makevol_execute",
     "makevol_params",
 ]