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

niwrap_afni/afni/v_2perm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_2PERM_METADATA = Metadata(
-    id="28ec035abc2bb2469bea6827599cc10fb826ba3c.boutiques",
+    id="540f8e1f8b85823bcf0dba52846ee4ef33340eca.boutiques",
     name="2perm",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_2PERM_METADATA = Metadata(
 
 
 V2permParameters = typing.TypedDict('V2permParameters', {
-    "__STYXTYPE__": typing.Literal["2perm"],
+    "@type": typing.NotRequired[typing.Literal["afni/2perm"]],
+    "prefix": typing.NotRequired[str | None],
+    "comma": bool,
+    "bottom_int": float,
+    "top_int": float,
+    "subset1_size": typing.NotRequired[float | None],
+    "subset2_size": typing.NotRequired[float | None],
+})
+V2permParametersTagged = typing.TypedDict('V2permParametersTagged', {
+    "@type": typing.Literal["afni/2perm"],
     "prefix": typing.NotRequired[str | None],
     "comma": bool,
     "bottom_int": float,
@@ -22,43 +31,11 @@ V2permParameters = typing.TypedDict('V2permParameters', {
     "subset1_size": typing.NotRequired[float | None],
     "subset2_size": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "2perm": v_2perm_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 {
-        "2perm": v_2perm_outputs,
-    }.get(t)
 
 
 class V2permOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_2perm(...)`.
+    Output object returned when calling `V2permParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v_2perm_params(
     comma: bool = False,
     subset1_size: float | None = None,
     subset2_size: float | None = None,
-) -> V2permParameters:
+) -> V2permParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def v_2perm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "2perm",
+        "@type": "afni/2perm",
         "comma": comma,
         "bottom_int": bottom_int,
         "top_int": top_int,
@@ -121,19 +98,19 @@ def v_2perm_cargs(
     """
     cargs = []
     cargs.append("2perm")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("comma"):
+    if params.get("comma", False):
         cargs.append("-comma")
-    cargs.append(str(params.get("bottom_int")))
-    cargs.append(str(params.get("top_int")))
-    if params.get("subset1_size") is not None:
-        cargs.append(str(params.get("subset1_size")))
-    if params.get("subset2_size") is not None:
-        cargs.append(str(params.get("subset2_size")))
+    cargs.append(str(params.get("bottom_int", None)))
+    cargs.append(str(params.get("top_int", None)))
+    if params.get("subset1_size", None) is not None:
+        cargs.append(str(params.get("subset1_size", None)))
+    if params.get("subset2_size", None) is not None:
+        cargs.append(str(params.get("subset2_size", None)))
     return cargs
 
 
@@ -152,17 +129,19 @@ def v_2perm_outputs(
     """
     ret = V2permOutputs(
         root=execution.output_file("."),
-        file_a=execution.output_file(params.get("prefix") + "_A") if (params.get("prefix") is not None) else None,
-        file_b=execution.output_file(params.get("prefix") + "_B") if (params.get("prefix") is not None) else None,
+        file_a=execution.output_file(params.get("prefix", None) + "_A") if (params.get("prefix") is not None) else None,
+        file_b=execution.output_file(params.get("prefix", None) + "_B") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_2perm_execute(
     params: V2permParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V2permOutputs:
     """
+    2perm
+    
     Generates two random non-overlapping subsets of a given set of integers.
     
     Author: AFNI Developers
@@ -171,10 +150,12 @@ def v_2perm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V2permOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_2PERM_METADATA)
     params = execution.params(params)
     cargs = v_2perm_cargs(params, execution)
     ret = v_2perm_outputs(params, execution)
@@ -192,6 +173,8 @@ def v_2perm(
     runner: Runner | None = None,
 ) -> V2permOutputs:
     """
+    2perm
+    
     Generates two random non-overlapping subsets of a given set of integers.
     
     Author: AFNI Developers
@@ -211,8 +194,6 @@ def v_2perm(
     Returns:
         NamedTuple of outputs (described in `V2permOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_2PERM_METADATA)
     params = v_2perm_params(
         prefix=prefix,
         comma=comma,
@@ -221,13 +202,13 @@ def v_2perm(
         subset1_size=subset1_size,
         subset2_size=subset2_size,
     )
-    return v_2perm_execute(params, execution)
+    return v_2perm_execute(params, runner)
 
 
 __all__ = [
     "V2permOutputs",
-    "V2permParameters",
     "V_2PERM_METADATA",
     "v_2perm",
+    "v_2perm_execute",
     "v_2perm_params",
 ]

niwrap_afni/afni/v_2swap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_2SWAP_METADATA = Metadata(
-    id="7816342873aa809adec96eabf2b229c9a0d64bcc.boutiques",
+    id="1615c69d084822a8eab97f58e6f163816f7a370b.boutiques",
     name="2swap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ V_2SWAP_METADATA = Metadata(
 
 
 V2swapParameters = typing.TypedDict('V2swapParameters', {
-    "__STYXTYPE__": typing.Literal["2swap"],
+    "@type": typing.NotRequired[typing.Literal["afni/2swap"]],
+    "quiet": bool,
+    "input_files": list[InputPathType],
+})
+V2swapParametersTagged = typing.TypedDict('V2swapParametersTagged', {
+    "@type": typing.Literal["afni/2swap"],
     "quiet": bool,
     "input_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "2swap": v_2swap_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 V2swapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_2swap(...)`.
+    Output object returned when calling `V2swapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class V2swapOutputs(typing.NamedTuple):
 def v_2swap_params(
     input_files: list[InputPathType],
     quiet: bool = False,
-) -> V2swapParameters:
+) -> V2swapParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def v_2swap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "2swap",
+        "@type": "afni/2swap",
         "quiet": quiet,
         "input_files": input_files,
     }
@@ -95,9 +69,9 @@ def v_2swap_cargs(
     """
     cargs = []
     cargs.append("2swap")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-q")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
     return cargs
 
 
@@ -122,9 +96,11 @@ def v_2swap_outputs(
 
 def v_2swap_execute(
     params: V2swapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V2swapOutputs:
     """
+    2swap
+    
     Swaps byte pairs on the files listed.
     
     Author: AFNI Developers
@@ -133,10 +109,12 @@ def v_2swap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V2swapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_2SWAP_METADATA)
     params = execution.params(params)
     cargs = v_2swap_cargs(params, execution)
     ret = v_2swap_outputs(params, execution)
@@ -150,6 +128,8 @@ def v_2swap(
     runner: Runner | None = None,
 ) -> V2swapOutputs:
     """
+    2swap
+    
     Swaps byte pairs on the files listed.
     
     Author: AFNI Developers
@@ -163,19 +143,17 @@ def v_2swap(
     Returns:
         NamedTuple of outputs (described in `V2swapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_2SWAP_METADATA)
     params = v_2swap_params(
         quiet=quiet,
         input_files=input_files,
     )
-    return v_2swap_execute(params, execution)
+    return v_2swap_execute(params, runner)
 
 
 __all__ = [
     "V2swapOutputs",
-    "V2swapParameters",
     "V_2SWAP_METADATA",
     "v_2swap",
+    "v_2swap_execute",
     "v_2swap_params",
 ]

niwrap_afni/afni/v_3d_aboverlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ABOVERLAP_METADATA = Metadata(
-    id="da965209d42fc668bebfda9fab7d92b0cef8fd70.boutiques",
+    id="38bc7ba550719cb365421b65b249f4f2cd07a334.boutiques",
     name="3dABoverlap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,26 @@ V_3D_ABOVERLAP_METADATA = Metadata(
 
 
 V3dAboverlapParameters = typing.TypedDict('V3dAboverlapParameters', {
-    "__STYXTYPE__": typing.Literal["3dABoverlap"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dABoverlap"]],
+    "dataset_a": InputPathType,
+    "dataset_b": InputPathType,
+    "no_automask": bool,
+    "quiet": bool,
+    "verbose": bool,
+})
+V3dAboverlapParametersTagged = typing.TypedDict('V3dAboverlapParametersTagged', {
+    "@type": typing.Literal["afni/3dABoverlap"],
     "dataset_a": InputPathType,
     "dataset_b": InputPathType,
     "no_automask": bool,
     "quiet": bool,
     "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 {
-        "3dABoverlap": v_3d_aboverlap_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 V3dAboverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_aboverlap(...)`.
+    Output object returned when calling `V3dAboverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def v_3d_aboverlap_params(
     no_automask: bool = False,
     quiet: bool = False,
     verbose: bool = False,
-) -> V3dAboverlapParameters:
+) -> V3dAboverlapParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +60,7 @@ def v_3d_aboverlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dABoverlap",
+        "@type": "afni/3dABoverlap",
         "dataset_a": dataset_a,
         "dataset_b": dataset_b,
         "no_automask": no_automask,
@@ -108,13 +85,13 @@ def v_3d_aboverlap_cargs(
     """
     cargs = []
     cargs.append("3dABoverlap")
-    cargs.append(execution.input_file(params.get("dataset_a")))
-    cargs.append(execution.input_file(params.get("dataset_b")))
-    if params.get("no_automask"):
+    cargs.append(execution.input_file(params.get("dataset_a", None)))
+    cargs.append(execution.input_file(params.get("dataset_b", None)))
+    if params.get("no_automask", False):
         cargs.append("-no_automask")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -140,11 +117,13 @@ def v_3d_aboverlap_outputs(
 
 def v_3d_aboverlap_execute(
     params: V3dAboverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAboverlapOutputs:
     """
-    Counts various metrics about how the automasks of datasets A and B overlap or
-    don't overlap.
+    3dABoverlap
+    
+    Counts various metrics about how the automasks of datasets A and B overlap
+    or don't overlap.
     
     Author: AFNI Developers
     
@@ -152,10 +131,12 @@ def v_3d_aboverlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAboverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ABOVERLAP_METADATA)
     params = execution.params(params)
     cargs = v_3d_aboverlap_cargs(params, execution)
     ret = v_3d_aboverlap_outputs(params, execution)
@@ -172,8 +153,10 @@ def v_3d_aboverlap(
     runner: Runner | None = None,
 ) -> V3dAboverlapOutputs:
     """
-    Counts various metrics about how the automasks of datasets A and B overlap or
-    don't overlap.
+    3dABoverlap
+    
+    Counts various metrics about how the automasks of datasets A and B overlap
+    or don't overlap.
     
     Author: AFNI Developers
     
@@ -190,8 +173,6 @@ def v_3d_aboverlap(
     Returns:
         NamedTuple of outputs (described in `V3dAboverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ABOVERLAP_METADATA)
     params = v_3d_aboverlap_params(
         dataset_a=dataset_a,
         dataset_b=dataset_b,
@@ -199,13 +180,13 @@ def v_3d_aboverlap(
         quiet=quiet,
         verbose=verbose,
     )
-    return v_3d_aboverlap_execute(params, execution)
+    return v_3d_aboverlap_execute(params, runner)
 
 
 __all__ = [
     "V3dAboverlapOutputs",
-    "V3dAboverlapParameters",
     "V_3D_ABOVERLAP_METADATA",
     "v_3d_aboverlap",
+    "v_3d_aboverlap_execute",
     "v_3d_aboverlap_params",
 ]

niwrap_afni/afni/v_3d_acost.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ACOST_METADATA = Metadata(
-    id="3b13cb783a9f1117e8f3b02cc3c2980e9a683a89.boutiques",
+    id="fb3855e6f92d078b083300d1163cbfd9b7712778.boutiques",
     name="3dAcost",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_ACOST_METADATA = Metadata(
 
 
 V3dAcostParameters = typing.TypedDict('V3dAcostParameters', {
-    "__STYXTYPE__": typing.Literal["3dAcost"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAcost"]],
+    "infile": InputPathType,
+    "basefile": InputPathType,
+    "outfile": str,
+    "all_cost": bool,
+})
+V3dAcostParametersTagged = typing.TypedDict('V3dAcostParametersTagged', {
+    "@type": typing.Literal["afni/3dAcost"],
     "infile": InputPathType,
     "basefile": InputPathType,
     "outfile": str,
     "all_cost": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAcost": v_3d_acost_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 {
-        "3dAcost": v_3d_acost_outputs,
-    }.get(t)
 
 
 class V3dAcostOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_acost(...)`.
+    Output object returned when calling `V3dAcostParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +46,7 @@ def v_3d_acost_params(
     basefile: InputPathType,
     outfile: str,
     all_cost: bool = False,
-) -> V3dAcostParameters:
+) -> V3dAcostParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def v_3d_acost_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAcost",
+        "@type": "afni/3dAcost",
         "infile": infile,
         "basefile": basefile,
         "outfile": outfile,
@@ -108,16 +83,16 @@ def v_3d_acost_cargs(
     """
     cargs = []
     cargs.append("3dAcost")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     cargs.extend([
         "-base",
-        execution.input_file(params.get("basefile"))
+        execution.input_file(params.get("basefile", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("outfile")
+        params.get("outfile", None)
     ])
-    if params.get("all_cost"):
+    if params.get("all_cost", False):
         cargs.append("-allcostX")
     return cargs
 
@@ -137,17 +112,19 @@ def v_3d_acost_outputs(
     """
     ret = V3dAcostOutputs(
         root=execution.output_file("."),
-        output_head=execution.output_file(params.get("outfile") + "+orig.HEAD"),
-        output_brik=execution.output_file(params.get("outfile") + "+orig.BRIK"),
+        output_head=execution.output_file(params.get("outfile", None) + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("outfile", None) + "+orig.BRIK"),
     )
     return ret
 
 
 def v_3d_acost_execute(
     params: V3dAcostParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAcostOutputs:
     """
+    3dAcost
+    
     Allineate dataset to a base dataset.
     
     Author: AFNI Developers
@@ -156,10 +133,12 @@ def v_3d_acost_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAcostOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ACOST_METADATA)
     params = execution.params(params)
     cargs = v_3d_acost_cargs(params, execution)
     ret = v_3d_acost_outputs(params, execution)
@@ -175,6 +154,8 @@ def v_3d_acost(
     runner: Runner | None = None,
 ) -> V3dAcostOutputs:
     """
+    3dAcost
+    
     Allineate dataset to a base dataset.
     
     Author: AFNI Developers
@@ -190,21 +171,19 @@ def v_3d_acost(
     Returns:
         NamedTuple of outputs (described in `V3dAcostOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ACOST_METADATA)
     params = v_3d_acost_params(
         infile=infile,
         basefile=basefile,
         outfile=outfile,
         all_cost=all_cost,
     )
-    return v_3d_acost_execute(params, execution)
+    return v_3d_acost_execute(params, runner)
 
 
 __all__ = [
     "V3dAcostOutputs",
-    "V3dAcostParameters",
     "V_3D_ACOST_METADATA",
     "v_3d_acost",
+    "v_3d_acost_execute",
     "v_3d_acost_params",
 ]