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

niwrap_afni/afni/inspec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INSPEC_METADATA = Metadata(
-    id="89203ff038bd27aa4191bdef00850e222bfaf10c.boutiques",
+    id="f3c02766faf70bafac4841d4ad24b734660a6873.boutiques",
     name="inspec",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ INSPEC_METADATA = Metadata(
 
 
 InspecParameters = typing.TypedDict('InspecParameters', {
-    "__STYXTYPE__": typing.Literal["inspec"],
+    "@type": typing.NotRequired[typing.Literal["afni/inspec"]],
+    "specfile": InputPathType,
+    "newspecname": typing.NotRequired[str | None],
+    "detail": typing.NotRequired[float | None],
+    "leftspec": typing.NotRequired[InputPathType | None],
+    "rightspec": typing.NotRequired[InputPathType | None],
+    "state_rm": typing.NotRequired[str | None],
+    "help": bool,
+})
+InspecParametersTagged = typing.TypedDict('InspecParametersTagged', {
+    "@type": typing.Literal["afni/inspec"],
     "specfile": InputPathType,
     "newspecname": typing.NotRequired[str | None],
     "detail": typing.NotRequired[float | None],
@@ -23,42 +33,11 @@ InspecParameters = typing.TypedDict('InspecParameters', {
     "state_rm": typing.NotRequired[str | None],
     "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 {
-        "inspec": inspec_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 InspecOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `inspec(...)`.
+    Output object returned when calling `InspecParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def inspec_params(
     rightspec: InputPathType | None = None,
     state_rm: str | None = None,
     help_: bool = False,
-) -> InspecParameters:
+) -> InspecParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +70,7 @@ def inspec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "inspec",
+        "@type": "afni/inspec",
         "specfile": specfile,
         "help": help_,
     }
@@ -125,34 +104,34 @@ def inspec_cargs(
     cargs.append("inspec")
     cargs.extend([
         "-spec",
-        execution.input_file(params.get("specfile"))
+        execution.input_file(params.get("specfile", None))
     ])
-    if params.get("newspecname") is not None:
+    if params.get("newspecname", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("newspecname")
+            params.get("newspecname", None)
         ])
-    if params.get("detail") is not None:
+    if params.get("detail", None) is not None:
         cargs.extend([
             "-detail",
-            str(params.get("detail"))
+            str(params.get("detail", None))
         ])
-    if params.get("leftspec") is not None:
+    if params.get("leftspec", None) is not None:
         cargs.extend([
             "-LRmerge",
-            execution.input_file(params.get("leftspec"))
+            execution.input_file(params.get("leftspec", None))
         ])
-    if params.get("rightspec") is not None:
+    if params.get("rightspec", None) is not None:
         cargs.extend([
             "-LRmerge",
-            execution.input_file(params.get("rightspec"))
+            execution.input_file(params.get("rightspec", None))
         ])
-    if params.get("state_rm") is not None:
+    if params.get("state_rm", None) is not None:
         cargs.extend([
             "-remove_state",
-            params.get("state_rm")
+            params.get("state_rm", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -178,9 +157,11 @@ def inspec_outputs(
 
 def inspec_execute(
     params: InspecParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> InspecOutputs:
     """
+    inspec
+    
     Outputs information found from specfile.
     
     Author: AFNI Developers
@@ -189,10 +170,12 @@ def inspec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InspecOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INSPEC_METADATA)
     params = execution.params(params)
     cargs = inspec_cargs(params, execution)
     ret = inspec_outputs(params, execution)
@@ -211,6 +194,8 @@ def inspec(
     runner: Runner | None = None,
 ) -> InspecOutputs:
     """
+    inspec
+    
     Outputs information found from specfile.
     
     Author: AFNI Developers
@@ -232,8 +217,6 @@ def inspec(
     Returns:
         NamedTuple of outputs (described in `InspecOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(INSPEC_METADATA)
     params = inspec_params(
         specfile=specfile,
         newspecname=newspecname,
@@ -243,13 +226,13 @@ def inspec(
         state_rm=state_rm,
         help_=help_,
     )
-    return inspec_execute(params, execution)
+    return inspec_execute(params, runner)
 
 
 __all__ = [
     "INSPEC_METADATA",
     "InspecOutputs",
-    "InspecParameters",
     "inspec",
+    "inspec_execute",
     "inspec_params",
 ]

niwrap_afni/afni/iso_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ISO_SURFACE_METADATA = Metadata(
-    id="891f1d7b5d35cf767a77b8a6bbe7028a6cad880f.boutiques",
+    id="97d44cc73a450dd708c49801cabdc7adefa67264.boutiques",
     name="IsoSurface",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ ISO_SURFACE_METADATA = Metadata(
 
 
 IsoSurfaceParameters = typing.TypedDict('IsoSurfaceParameters', {
-    "__STYXTYPE__": typing.Literal["IsoSurface"],
+    "@type": typing.NotRequired[typing.Literal["afni/IsoSurface"]],
+    "input_vol": typing.NotRequired[InputPathType | None],
+    "shape_spec": typing.NotRequired[list[str] | None],
+    "isorois": bool,
+    "isoval": typing.NotRequired[str | None],
+    "isorange": typing.NotRequired[list[str] | None],
+    "isocmask": typing.NotRequired[str | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "tsmooth": typing.NotRequired[list[str] | None],
+    "debug": typing.NotRequired[str | None],
+    "autocrop": bool,
+    "remesh": typing.NotRequired[str | None],
+    "xform": typing.NotRequired[str | None],
+    "novolreg": bool,
+    "noxform": bool,
+})
+IsoSurfaceParametersTagged = typing.TypedDict('IsoSurfaceParametersTagged', {
+    "@type": typing.Literal["afni/IsoSurface"],
     "input_vol": typing.NotRequired[InputPathType | None],
     "shape_spec": typing.NotRequired[list[str] | None],
     "isorois": bool,
@@ -30,43 +47,11 @@ IsoSurfaceParameters = typing.TypedDict('IsoSurfaceParameters', {
     "novolreg": bool,
     "noxform": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "IsoSurface": iso_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 {
-        "IsoSurface": iso_surface_outputs,
-    }.get(t)
 
 
 class IsoSurfaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `iso_surface(...)`.
+    Output object returned when calling `IsoSurfaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def iso_surface_params(
     xform: str | None = None,
     novolreg: bool = False,
     noxform: bool = False,
-) -> IsoSurfaceParameters:
+) -> IsoSurfaceParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +103,7 @@ def iso_surface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "IsoSurface",
+        "@type": "afni/IsoSurface",
         "isorois": isorois,
         "autocrop": autocrop,
         "novolreg": novolreg,
@@ -162,63 +147,63 @@ def iso_surface_cargs(
     """
     cargs = []
     cargs.append("IsoSurface")
-    if params.get("input_vol") is not None:
+    if params.get("input_vol", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("input_vol"))
+            execution.input_file(params.get("input_vol", None))
         ])
-    if params.get("shape_spec") is not None:
+    if params.get("shape_spec", None) is not None:
         cargs.extend([
             "-shape",
-            *params.get("shape_spec")
+            *params.get("shape_spec", None)
         ])
-    if params.get("isorois"):
+    if params.get("isorois", False):
         cargs.append("-isorois")
-    if params.get("isoval") is not None:
+    if params.get("isoval", None) is not None:
         cargs.extend([
             "-isoval",
-            params.get("isoval")
+            params.get("isoval", None)
         ])
-    if params.get("isorange") is not None:
+    if params.get("isorange", None) is not None:
         cargs.extend([
             "-isorange",
-            *params.get("isorange")
+            *params.get("isorange", None)
         ])
-    if params.get("isocmask") is not None:
+    if params.get("isocmask", None) is not None:
         cargs.extend([
             "-isocmask",
-            params.get("isocmask")
+            params.get("isocmask", None)
         ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-o_TYPE",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("tsmooth") is not None:
+    if params.get("tsmooth", None) is not None:
         cargs.extend([
             "-Tsmooth",
-            *params.get("tsmooth")
+            *params.get("tsmooth", None)
         ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            params.get("debug")
+            params.get("debug", None)
         ])
-    if params.get("autocrop"):
+    if params.get("autocrop", False):
         cargs.append("-autocrop")
-    if params.get("remesh") is not None:
+    if params.get("remesh", None) is not None:
         cargs.extend([
             "-remesh",
-            params.get("remesh")
+            params.get("remesh", None)
         ])
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            params.get("xform")
+            params.get("xform", None)
         ])
-    if params.get("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("noxform"):
+    if params.get("noxform", False):
         cargs.append("-noxform")
     return cargs
 
@@ -247,9 +232,11 @@ def iso_surface_outputs(
 
 def iso_surface_execute(
     params: IsoSurfaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsoSurfaceOutputs:
     """
+    IsoSurface
+    
     A program to perform isosurface extraction from a volume.
     
     Author: AFNI Developers
@@ -258,10 +245,12 @@ def iso_surface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsoSurfaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ISO_SURFACE_METADATA)
     params = execution.params(params)
     cargs = iso_surface_cargs(params, execution)
     ret = iso_surface_outputs(params, execution)
@@ -287,6 +276,8 @@ def iso_surface(
     runner: Runner | None = None,
 ) -> IsoSurfaceOutputs:
     """
+    IsoSurface
+    
     A program to perform isosurface extraction from a volume.
     
     Author: AFNI Developers
@@ -314,8 +305,6 @@ def iso_surface(
     Returns:
         NamedTuple of outputs (described in `IsoSurfaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ISO_SURFACE_METADATA)
     params = iso_surface_params(
         input_vol=input_vol,
         shape_spec=shape_spec,
@@ -332,13 +321,13 @@ def iso_surface(
         novolreg=novolreg,
         noxform=noxform,
     )
-    return iso_surface_execute(params, execution)
+    return iso_surface_execute(params, runner)
 
 
 __all__ = [
     "ISO_SURFACE_METADATA",
     "IsoSurfaceOutputs",
-    "IsoSurfaceParameters",
     "iso_surface",
+    "iso_surface_execute",
     "iso_surface_params",
 ]