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

niwrap_afni/afni/suma_change_spec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SUMA_CHANGE_SPEC_METADATA = Metadata(
-    id="f13f0176c0f78fdf29d29c5c7899209d6deff415.boutiques",
+    id="f205472e4606b6817b176ca699e0bc449e4cfb0f.boutiques",
     name="suma_change_spec",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ SUMA_CHANGE_SPEC_METADATA = Metadata(
 
 
 SumaChangeSpecParameters = typing.TypedDict('SumaChangeSpecParameters', {
-    "__STYXTYPE__": typing.Literal["suma_change_spec"],
+    "@type": typing.NotRequired[typing.Literal["afni/suma_change_spec"]],
+    "input": InputPathType,
+    "state": str,
+    "domainparent": typing.NotRequired[str | None],
+    "output": typing.NotRequired[str | None],
+    "remove": bool,
+    "anatomical": bool,
+})
+SumaChangeSpecParametersTagged = typing.TypedDict('SumaChangeSpecParametersTagged', {
+    "@type": typing.Literal["afni/suma_change_spec"],
     "input": InputPathType,
     "state": str,
     "domainparent": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ SumaChangeSpecParameters = typing.TypedDict('SumaChangeSpecParameters', {
     "remove": bool,
     "anatomical": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "suma_change_spec": suma_change_spec_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 {
-        "suma_change_spec": suma_change_spec_outputs,
-    }.get(t)
 
 
 class SumaChangeSpecOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `suma_change_spec(...)`.
+    Output object returned when calling `SumaChangeSpecParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def suma_change_spec_params(
     output: str | None = None,
     remove: bool = False,
     anatomical: bool = False,
-) -> SumaChangeSpecParameters:
+) -> SumaChangeSpecParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def suma_change_spec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "suma_change_spec",
+        "@type": "afni/suma_change_spec",
         "input": input_,
         "state": state,
         "remove": remove,
@@ -118,15 +95,15 @@ def suma_change_spec_cargs(
     """
     cargs = []
     cargs.append("suma_change_spec")
-    cargs.append(execution.input_file(params.get("input")))
-    cargs.append(params.get("state"))
-    if params.get("domainparent") is not None:
-        cargs.append(params.get("domainparent"))
-    if params.get("output") is not None:
-        cargs.append(params.get("output"))
-    if params.get("remove"):
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("state", None))
+    if params.get("domainparent", None) is not None:
+        cargs.append(params.get("domainparent", None))
+    if params.get("output", None) is not None:
+        cargs.append(params.get("output", None))
+    if params.get("remove", False):
         cargs.append("-remove")
-    if params.get("anatomical"):
+    if params.get("anatomical", False):
         cargs.append("-anatomical")
     return cargs
 
@@ -146,17 +123,19 @@ def suma_change_spec_outputs(
     """
     ret = SumaChangeSpecOutputs(
         root=execution.output_file("."),
-        output_spec=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
-        backup_spec=execution.output_file(pathlib.Path(params.get("input")).name + ".bkp"),
+        output_spec=execution.output_file(params.get("output", None)) if (params.get("output") is not None) else None,
+        backup_spec=execution.output_file(pathlib.Path(params.get("input", None)).name + ".bkp"),
     )
     return ret
 
 
 def suma_change_spec_execute(
     params: SumaChangeSpecParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SumaChangeSpecOutputs:
     """
+    suma_change_spec
+    
     This program changes SUMA's surface specification (Spec) files.
     
     Author: AFNI Developers
@@ -165,10 +144,12 @@ def suma_change_spec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SumaChangeSpecOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SUMA_CHANGE_SPEC_METADATA)
     params = execution.params(params)
     cargs = suma_change_spec_cargs(params, execution)
     ret = suma_change_spec_outputs(params, execution)
@@ -186,6 +167,8 @@ def suma_change_spec(
     runner: Runner | None = None,
 ) -> SumaChangeSpecOutputs:
     """
+    suma_change_spec
+    
     This program changes SUMA's surface specification (Spec) files.
     
     Author: AFNI Developers
@@ -203,8 +186,6 @@ def suma_change_spec(
     Returns:
         NamedTuple of outputs (described in `SumaChangeSpecOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SUMA_CHANGE_SPEC_METADATA)
     params = suma_change_spec_params(
         input_=input_,
         state=state,
@@ -213,13 +194,13 @@ def suma_change_spec(
         remove=remove,
         anatomical=anatomical,
     )
-    return suma_change_spec_execute(params, execution)
+    return suma_change_spec_execute(params, runner)
 
 
 __all__ = [
     "SUMA_CHANGE_SPEC_METADATA",
     "SumaChangeSpecOutputs",
-    "SumaChangeSpecParameters",
     "suma_change_spec",
+    "suma_change_spec_execute",
     "suma_change_spec_params",
 ]

niwrap_afni/afni/suma_glxdino.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SUMA_GLXDINO_METADATA = Metadata(
-    id="db20e466e60a0e5e1fdf389e067115a796b337a4.boutiques",
+    id="ff8213640ad8c997c8565a4312bacb57bfcc0bcd.boutiques",
     name="SUMA_glxdino",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,45 +14,18 @@ SUMA_GLXDINO_METADATA = Metadata(
 
 
 SumaGlxdinoParameters = typing.TypedDict('SumaGlxdinoParameters', {
-    "__STYXTYPE__": typing.Literal["SUMA_glxdino"],
+    "@type": typing.NotRequired[typing.Literal["afni/SUMA_glxdino"]],
+    "verbose": bool,
+})
+SumaGlxdinoParametersTagged = typing.TypedDict('SumaGlxdinoParametersTagged', {
+    "@type": typing.Literal["afni/SUMA_glxdino"],
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SUMA_glxdino": suma_glxdino_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 SumaGlxdinoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `suma_glxdino(...)`.
+    Output object returned when calling `SumaGlxdinoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class SumaGlxdinoOutputs(typing.NamedTuple):
 
 def suma_glxdino_params(
     verbose: bool = False,
-) -> SumaGlxdinoParameters:
+) -> SumaGlxdinoParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def suma_glxdino_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SUMA_glxdino",
+        "@type": "afni/SUMA_glxdino",
         "verbose": verbose,
     }
     return params
@@ -91,7 +64,7 @@ def suma_glxdino_cargs(
     """
     cargs = []
     cargs.append("SUMA_glxdino")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
     return cargs
 
@@ -117,11 +90,13 @@ def suma_glxdino_outputs(
 
 def suma_glxdino_execute(
     params: SumaGlxdinoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SumaGlxdinoOutputs:
     """
-    A simple openGL test program using GLX. If it does not run, then SUMA certainly
-    won't.
+    SUMA_glxdino
+    
+    A simple openGL test program using GLX. If it does not run, then SUMA
+    certainly won't.
     
     Author: AFNI Developers
     
@@ -129,10 +104,12 @@ def suma_glxdino_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SumaGlxdinoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SUMA_GLXDINO_METADATA)
     params = execution.params(params)
     cargs = suma_glxdino_cargs(params, execution)
     ret = suma_glxdino_outputs(params, execution)
@@ -145,8 +122,10 @@ def suma_glxdino(
     runner: Runner | None = None,
 ) -> SumaGlxdinoOutputs:
     """
-    A simple openGL test program using GLX. If it does not run, then SUMA certainly
-    won't.
+    SUMA_glxdino
+    
+    A simple openGL test program using GLX. If it does not run, then SUMA
+    certainly won't.
     
     Author: AFNI Developers
     
@@ -158,18 +137,16 @@ def suma_glxdino(
     Returns:
         NamedTuple of outputs (described in `SumaGlxdinoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SUMA_GLXDINO_METADATA)
     params = suma_glxdino_params(
         verbose=verbose,
     )
-    return suma_glxdino_execute(params, execution)
+    return suma_glxdino_execute(params, runner)
 
 
 __all__ = [
     "SUMA_GLXDINO_METADATA",
     "SumaGlxdinoOutputs",
-    "SumaGlxdinoParameters",
     "suma_glxdino",
+    "suma_glxdino_execute",
     "suma_glxdino_params",
 ]

niwrap_afni/afni/surf2_vol_coord.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF2_VOL_COORD_METADATA = Metadata(
-    id="6fe6474a33c8e23675d3aa29e680feb2c2b37bc1.boutiques",
+    id="83f5c27753a488afc50b351a43a27d3604840686.boutiques",
     name="Surf2VolCoord",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ SURF2_VOL_COORD_METADATA = Metadata(
 
 
 Surf2VolCoordParameters = typing.TypedDict('Surf2VolCoordParameters', {
-    "__STYXTYPE__": typing.Literal["Surf2VolCoord"],
+    "@type": typing.NotRequired[typing.Literal["afni/Surf2VolCoord"]],
+    "surface": str,
+    "grid_vol": InputPathType,
+    "grid_subbrick": typing.NotRequired[float | None],
+    "sv": typing.NotRequired[InputPathType | None],
+    "one_node": typing.NotRequired[str | None],
+    "closest_nodes": InputPathType,
+    "qual": typing.NotRequired[str | None],
+    "lpi": bool,
+    "rai": bool,
+    "verb_level": typing.NotRequired[float | None],
+    "prefix": str,
+})
+Surf2VolCoordParametersTagged = typing.TypedDict('Surf2VolCoordParametersTagged', {
+    "@type": typing.Literal["afni/Surf2VolCoord"],
     "surface": str,
     "grid_vol": InputPathType,
     "grid_subbrick": typing.NotRequired[float | None],
@@ -27,43 +41,11 @@ Surf2VolCoordParameters = typing.TypedDict('Surf2VolCoordParameters', {
     "verb_level": typing.NotRequired[float | None],
     "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 {
-        "Surf2VolCoord": surf2_vol_coord_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 {
-        "Surf2VolCoord": surf2_vol_coord_outputs,
-    }.get(t)
 
 
 class Surf2VolCoordOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf2_vol_coord(...)`.
+    Output object returned when calling `Surf2VolCoordParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def surf2_vol_coord_params(
     lpi: bool = False,
     rai: bool = False,
     verb_level: float | None = None,
-) -> Surf2VolCoordParameters:
+) -> Surf2VolCoordParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +89,7 @@ def surf2_vol_coord_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "Surf2VolCoord",
+        "@type": "afni/Surf2VolCoord",
         "surface": surface,
         "grid_vol": grid_vol,
         "closest_nodes": closest_nodes,
@@ -145,48 +127,48 @@ def surf2_vol_coord_cargs(
     cargs.append("Surf2VolCoord")
     cargs.extend([
         "-i_TYPE",
-        params.get("surface")
+        params.get("surface", None)
     ])
     cargs.extend([
         "-grid_parent",
-        execution.input_file(params.get("grid_vol"))
+        execution.input_file(params.get("grid_vol", None))
     ])
-    if params.get("grid_subbrick") is not None:
+    if params.get("grid_subbrick", None) is not None:
         cargs.extend([
             "-grid_subbrick",
-            str(params.get("grid_subbrick"))
+            str(params.get("grid_subbrick", None))
         ])
-    if params.get("sv") is not None:
+    if params.get("sv", None) is not None:
         cargs.extend([
             "-sv",
-            execution.input_file(params.get("sv"))
+            execution.input_file(params.get("sv", None))
         ])
-    if params.get("one_node") is not None:
+    if params.get("one_node", None) is not None:
         cargs.extend([
             "-one_node",
-            params.get("one_node")
+            params.get("one_node", None)
         ])
     cargs.extend([
         "-closest_nodes",
-        execution.input_file(params.get("closest_nodes"))
+        execution.input_file(params.get("closest_nodes", None))
     ])
-    if params.get("qual") is not None:
+    if params.get("qual", None) is not None:
         cargs.extend([
             "-qual",
-            params.get("qual")
+            params.get("qual", None)
         ])
-    if params.get("lpi"):
+    if params.get("lpi", False):
         cargs.append("-LPI")
-    if params.get("rai"):
+    if params.get("rai", False):
         cargs.append("-RAI")
-    if params.get("verb_level") is not None:
+    if params.get("verb_level", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verb_level"))
+            str(params.get("verb_level", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     return cargs
 
@@ -206,16 +188,18 @@ def surf2_vol_coord_outputs(
     """
     ret = Surf2VolCoordOutputs(
         root=execution.output_file("."),
-        results_file=execution.output_file(params.get("prefix")),
+        results_file=execution.output_file(params.get("prefix", None)),
     )
     return ret
 
 
 def surf2_vol_coord_execute(
     params: Surf2VolCoordParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Surf2VolCoordOutputs:
     """
+    Surf2VolCoord
+    
     Relates node indices to coordinates given x y z coordinates and returns the
     nodes closest to them.
     
@@ -225,10 +209,12 @@ def surf2_vol_coord_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Surf2VolCoordOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF2_VOL_COORD_METADATA)
     params = execution.params(params)
     cargs = surf2_vol_coord_cargs(params, execution)
     ret = surf2_vol_coord_outputs(params, execution)
@@ -251,6 +237,8 @@ def surf2_vol_coord(
     runner: Runner | None = None,
 ) -> Surf2VolCoordOutputs:
     """
+    Surf2VolCoord
+    
     Relates node indices to coordinates given x y z coordinates and returns the
     nodes closest to them.
     
@@ -278,8 +266,6 @@ def surf2_vol_coord(
     Returns:
         NamedTuple of outputs (described in `Surf2VolCoordOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF2_VOL_COORD_METADATA)
     params = surf2_vol_coord_params(
         surface=surface,
         grid_vol=grid_vol,
@@ -293,13 +279,13 @@ def surf2_vol_coord(
         verb_level=verb_level,
         prefix=prefix,
     )
-    return surf2_vol_coord_execute(params, execution)
+    return surf2_vol_coord_execute(params, runner)
 
 
 __all__ = [
     "SURF2_VOL_COORD_METADATA",
     "Surf2VolCoordOutputs",
-    "Surf2VolCoordParameters",
     "surf2_vol_coord",
+    "surf2_vol_coord_execute",
     "surf2_vol_coord_params",
 ]