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

niwrap_afni/afni/v_3d_tortoiseto_here.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TORTOISETO_HERE_METADATA = Metadata(
-    id="b586a66e7c8cb3276d689bcfab9e2b865e81f3ea.boutiques",
+    id="83f9aa471eb814950e17357d5882b341f95fdb2b.boutiques",
     name="3dTORTOISEtoHere",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_TORTOISETO_HERE_METADATA = Metadata(
 
 
 V3dTortoisetoHereParameters = typing.TypedDict('V3dTortoisetoHereParameters', {
-    "__STYXTYPE__": typing.Literal["3dTORTOISEtoHere"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTORTOISEtoHere"]],
+    "dt_tort": InputPathType,
+    "prefix": str,
+    "scale_factor": typing.NotRequired[float | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+})
+V3dTortoisetoHereParametersTagged = typing.TypedDict('V3dTortoisetoHereParametersTagged', {
+    "@type": typing.Literal["afni/3dTORTOISEtoHere"],
     "dt_tort": InputPathType,
     "prefix": str,
     "scale_factor": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ V3dTortoisetoHereParameters = typing.TypedDict('V3dTortoisetoHereParameters', {
     "flip_y": bool,
     "flip_z": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTORTOISEtoHere": v_3d_tortoiseto_here_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 {
-        "3dTORTOISEtoHere": v_3d_tortoiseto_here_outputs,
-    }.get(t)
 
 
 class V3dTortoisetoHereOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tortoiseto_here(...)`.
+    Output object returned when calling `V3dTortoisetoHereParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +51,7 @@ def v_3d_tortoiseto_here_params(
     flip_x: bool = False,
     flip_y: bool = False,
     flip_z: bool = False,
-) -> V3dTortoisetoHereParameters:
+) -> V3dTortoisetoHereParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def v_3d_tortoiseto_here_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTORTOISEtoHere",
+        "@type": "afni/3dTORTOISEtoHere",
         "dt_tort": dt_tort,
         "prefix": prefix,
         "flip_x": flip_x,
@@ -121,22 +98,22 @@ def v_3d_tortoiseto_here_cargs(
     cargs.append("3dTORTOISEtoHere")
     cargs.extend([
         "-dt_tort",
-        execution.input_file(params.get("dt_tort"))
+        execution.input_file(params.get("dt_tort", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("scale_factor") is not None:
+    if params.get("scale_factor", None) is not None:
         cargs.extend([
             "-scale_fac",
-            str(params.get("scale_factor"))
+            str(params.get("scale_factor", None))
         ])
-    if params.get("flip_x"):
+    if params.get("flip_x", False):
         cargs.append("-flip_x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-flip_y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-flip_z")
     return cargs
 
@@ -156,18 +133,20 @@ def v_3d_tortoiseto_here_outputs(
     """
     ret = V3dTortoisetoHereOutputs(
         root=execution.output_file("."),
-        output_dt_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output_dt_file=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_tortoiseto_here_execute(
     params: V3dTortoisetoHereParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTortoisetoHereOutputs:
     """
-    Convert standard TORTOISE DTs (diagonal-first format) to standard AFNI (lower
-    triangular, row-wise) format.
+    3dTORTOISEtoHere
+    
+    Convert standard TORTOISE DTs (diagonal-first format) to standard AFNI
+    (lower triangular, row-wise) format.
     
     Author: AFNI Developers
     
@@ -175,10 +154,12 @@ def v_3d_tortoiseto_here_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTortoisetoHereOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TORTOISETO_HERE_METADATA)
     params = execution.params(params)
     cargs = v_3d_tortoiseto_here_cargs(params, execution)
     ret = v_3d_tortoiseto_here_outputs(params, execution)
@@ -196,8 +177,10 @@ def v_3d_tortoiseto_here(
     runner: Runner | None = None,
 ) -> V3dTortoisetoHereOutputs:
     """
-    Convert standard TORTOISE DTs (diagonal-first format) to standard AFNI (lower
-    triangular, row-wise) format.
+    3dTORTOISEtoHere
+    
+    Convert standard TORTOISE DTs (diagonal-first format) to standard AFNI
+    (lower triangular, row-wise) format.
     
     Author: AFNI Developers
     
@@ -217,8 +200,6 @@ def v_3d_tortoiseto_here(
     Returns:
         NamedTuple of outputs (described in `V3dTortoisetoHereOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TORTOISETO_HERE_METADATA)
     params = v_3d_tortoiseto_here_params(
         dt_tort=dt_tort,
         prefix=prefix,
@@ -227,13 +208,13 @@ def v_3d_tortoiseto_here(
         flip_y=flip_y,
         flip_z=flip_z,
     )
-    return v_3d_tortoiseto_here_execute(params, execution)
+    return v_3d_tortoiseto_here_execute(params, runner)
 
 
 __all__ = [
     "V3dTortoisetoHereOutputs",
-    "V3dTortoisetoHereParameters",
     "V_3D_TORTOISETO_HERE_METADATA",
     "v_3d_tortoiseto_here",
+    "v_3d_tortoiseto_here_execute",
     "v_3d_tortoiseto_here_params",
 ]

niwrap_afni/afni/v_3d_toutcount.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TOUTCOUNT_METADATA = Metadata(
-    id="76920b41e924975789eef980078cb1ea35d8f364.boutiques",
+    id="9193883305e8473f3547bb336f7df4ae106042f8.boutiques",
     name="3dToutcount",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V_3D_TOUTCOUNT_METADATA = Metadata(
 
 
 V3dToutcountParameters = typing.TypedDict('V3dToutcountParameters', {
-    "__STYXTYPE__": typing.Literal["3dToutcount"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dToutcount"]],
+    "input_dataset": str,
+    "output_prefix": typing.NotRequired[str | None],
+    "mask_dataset": typing.NotRequired[str | None],
+    "q_threshold": typing.NotRequired[float | None],
+    "autoclip": bool,
+    "automask": bool,
+    "fraction": bool,
+    "range": bool,
+    "polort_order": typing.NotRequired[float | None],
+    "legendre": bool,
+})
+V3dToutcountParametersTagged = typing.TypedDict('V3dToutcountParametersTagged', {
+    "@type": typing.Literal["afni/3dToutcount"],
     "input_dataset": str,
     "output_prefix": typing.NotRequired[str | None],
     "mask_dataset": typing.NotRequired[str | None],
@@ -26,43 +39,11 @@ V3dToutcountParameters = typing.TypedDict('V3dToutcountParameters', {
     "polort_order": typing.NotRequired[float | None],
     "legendre": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dToutcount": v_3d_toutcount_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 {
-        "3dToutcount": v_3d_toutcount_outputs,
-    }.get(t)
 
 
 class V3dToutcountOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_toutcount(...)`.
+    Output object returned when calling `V3dToutcountParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +64,7 @@ def v_3d_toutcount_params(
     range_: bool = False,
     polort_order: float | None = None,
     legendre: bool = False,
-) -> V3dToutcountParameters:
+) -> V3dToutcountParametersTagged:
     """
     Build parameters.
     
@@ -108,7 +89,7 @@ def v_3d_toutcount_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dToutcount",
+        "@type": "afni/3dToutcount",
         "input_dataset": input_dataset,
         "autoclip": autoclip,
         "automask": automask,
@@ -142,33 +123,33 @@ def v_3d_toutcount_cargs(
     """
     cargs = []
     cargs.append("3dToutcount")
-    cargs.append(params.get("input_dataset"))
-    if params.get("output_prefix") is not None:
-        cargs.append(params.get("output_prefix"))
-    if params.get("mask_dataset") is not None:
+    cargs.append(params.get("input_dataset", None))
+    if params.get("output_prefix", None) is not None:
+        cargs.append(params.get("output_prefix", None))
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask_dataset")
+            params.get("mask_dataset", None)
         ])
-    if params.get("q_threshold") is not None:
+    if params.get("q_threshold", None) is not None:
         cargs.extend([
             "-qthr",
-            str(params.get("q_threshold"))
+            str(params.get("q_threshold", None))
         ])
-    if params.get("autoclip"):
+    if params.get("autoclip", False):
         cargs.append("-autoclip")
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("fraction"):
+    if params.get("fraction", False):
         cargs.append("-fraction")
-    if params.get("range"):
+    if params.get("range", False):
         cargs.append("-range")
-    if params.get("polort_order") is not None:
+    if params.get("polort_order", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polort_order"))
+            str(params.get("polort_order", None))
         ])
-    if params.get("legendre"):
+    if params.get("legendre", False):
         cargs.append("-legendre")
     return cargs
 
@@ -188,17 +169,19 @@ def v_3d_toutcount_outputs(
     """
     ret = V3dToutcountOutputs(
         root=execution.output_file("."),
-        output_afni_head=execution.output_file(params.get("output_prefix") + ".HEAD") if (params.get("output_prefix") is not None) else None,
-        output_afni_brik=execution.output_file(params.get("output_prefix") + ".BRIK") if (params.get("output_prefix") is not None) else None,
+        output_afni_head=execution.output_file(params.get("output_prefix", None) + ".HEAD") if (params.get("output_prefix") is not None) else None,
+        output_afni_brik=execution.output_file(params.get("output_prefix", None) + ".BRIK") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_toutcount_execute(
     params: V3dToutcountParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dToutcountOutputs:
     """
+    3dToutcount
+    
     Calculates the number of 'outliers' in a 3D+time dataset at each time point.
     
     Author: AFNI Developers
@@ -207,10 +190,12 @@ def v_3d_toutcount_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dToutcountOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TOUTCOUNT_METADATA)
     params = execution.params(params)
     cargs = v_3d_toutcount_cargs(params, execution)
     ret = v_3d_toutcount_outputs(params, execution)
@@ -232,6 +217,8 @@ def v_3d_toutcount(
     runner: Runner | None = None,
 ) -> V3dToutcountOutputs:
     """
+    3dToutcount
+    
     Calculates the number of 'outliers' in a 3D+time dataset at each time point.
     
     Author: AFNI Developers
@@ -259,8 +246,6 @@ def v_3d_toutcount(
     Returns:
         NamedTuple of outputs (described in `V3dToutcountOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TOUTCOUNT_METADATA)
     params = v_3d_toutcount_params(
         input_dataset=input_dataset,
         output_prefix=output_prefix,
@@ -273,13 +258,13 @@ def v_3d_toutcount(
         polort_order=polort_order,
         legendre=legendre,
     )
-    return v_3d_toutcount_execute(params, execution)
+    return v_3d_toutcount_execute(params, runner)
 
 
 __all__ = [
     "V3dToutcountOutputs",
-    "V3dToutcountParameters",
     "V_3D_TOUTCOUNT_METADATA",
     "v_3d_toutcount",
+    "v_3d_toutcount_execute",
     "v_3d_toutcount_params",
 ]

niwrap_afni/afni/v_3d_toy_prog.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TOY_PROG_METADATA = Metadata(
-    id="5b79d4ff9e6891e041e9a3b68d176f2055097819.boutiques",
+    id="f250d1ab72c2eedeae35543aa257ea3a3ce9e74b.boutiques",
     name="3dToyProg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_TOY_PROG_METADATA = Metadata(
 
 
 V3dToyProgParameters = typing.TypedDict('V3dToyProgParameters', {
-    "__STYXTYPE__": typing.Literal["3dToyProg"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dToyProg"]],
+    "input_dataset": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "output_datum": typing.NotRequired[typing.Literal["float", "short"] | None],
+    "mini_help": bool,
+    "help": bool,
+    "extreme_help": bool,
+    "help_view": bool,
+    "help_web": bool,
+    "help_find": typing.NotRequired[str | None],
+    "help_raw": bool,
+    "help_spx": bool,
+    "help_aspx": bool,
+    "help_all_opts": bool,
+})
+V3dToyProgParametersTagged = typing.TypedDict('V3dToyProgParametersTagged', {
+    "@type": typing.Literal["afni/3dToyProg"],
     "input_dataset": InputPathType,
     "output_prefix": typing.NotRequired[str | None],
     "mask_dataset": typing.NotRequired[InputPathType | None],
@@ -30,42 +47,11 @@ V3dToyProgParameters = typing.TypedDict('V3dToyProgParameters', {
     "help_aspx": bool,
     "help_all_opts": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dToyProg": v_3d_toy_prog_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 V3dToyProgOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_toy_prog(...)`.
+    Output object returned when calling `V3dToyProgParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +72,7 @@ def v_3d_toy_prog_params(
     help_spx: bool = False,
     help_aspx: bool = False,
     help_all_opts: bool = False,
-) -> V3dToyProgParameters:
+) -> V3dToyProgParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +104,7 @@ def v_3d_toy_prog_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dToyProg",
+        "@type": "afni/3dToyProg",
         "input_dataset": input_dataset,
         "mini_help": mini_help,
         "help": help_,
@@ -158,45 +144,45 @@ def v_3d_toy_prog_cargs(
     cargs.append("3dToyProg")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("mask_dataset") is not None:
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_dataset"))
+            execution.input_file(params.get("mask_dataset", None))
         ])
-    if params.get("output_datum") is not None:
+    if params.get("output_datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("output_datum")
+            params.get("output_datum", None)
         ])
-    if params.get("mini_help"):
+    if params.get("mini_help", False):
         cargs.append("-h")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("extreme_help"):
+    if params.get("extreme_help", False):
         cargs.append("-HELP")
-    if params.get("help_view"):
+    if params.get("help_view", False):
         cargs.append("-h_view")
-    if params.get("help_web"):
+    if params.get("help_web", False):
         cargs.append("-h_web")
-    if params.get("help_find") is not None:
+    if params.get("help_find", None) is not None:
         cargs.extend([
             "-h_find",
-            params.get("help_find")
+            params.get("help_find", None)
         ])
-    if params.get("help_raw"):
+    if params.get("help_raw", False):
         cargs.append("-h_raw")
-    if params.get("help_spx"):
+    if params.get("help_spx", False):
         cargs.append("-h_spx")
-    if params.get("help_aspx"):
+    if params.get("help_aspx", False):
         cargs.append("-h_aspx")
-    if params.get("help_all_opts"):
+    if params.get("help_all_opts", False):
         cargs.append("-all_opts")
     return cargs
 
@@ -222,10 +208,13 @@ def v_3d_toy_prog_outputs(
 
 def v_3d_toy_prog_execute(
     params: V3dToyProgParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dToyProgOutputs:
     """
-    A program to illustrate dataset creation and manipulation in C using AFNI's API.
+    3dToyProg
+    
+    A program to illustrate dataset creation and manipulation in C using AFNI's
+    API.
     
     Author: AFNI Developers
     
@@ -233,10 +222,12 @@ def v_3d_toy_prog_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dToyProgOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TOY_PROG_METADATA)
     params = execution.params(params)
     cargs = v_3d_toy_prog_cargs(params, execution)
     ret = v_3d_toy_prog_outputs(params, execution)
@@ -262,7 +253,10 @@ def v_3d_toy_prog(
     runner: Runner | None = None,
 ) -> V3dToyProgOutputs:
     """
-    A program to illustrate dataset creation and manipulation in C using AFNI's API.
+    3dToyProg
+    
+    A program to illustrate dataset creation and manipulation in C using AFNI's
+    API.
     
     Author: AFNI Developers
     
@@ -296,8 +290,6 @@ def v_3d_toy_prog(
     Returns:
         NamedTuple of outputs (described in `V3dToyProgOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TOY_PROG_METADATA)
     params = v_3d_toy_prog_params(
         input_dataset=input_dataset,
         output_prefix=output_prefix,
@@ -314,13 +306,13 @@ def v_3d_toy_prog(
         help_aspx=help_aspx,
         help_all_opts=help_all_opts,
     )
-    return v_3d_toy_prog_execute(params, execution)
+    return v_3d_toy_prog_execute(params, runner)
 
 
 __all__ = [
     "V3dToyProgOutputs",
-    "V3dToyProgParameters",
     "V_3D_TOY_PROG_METADATA",
     "v_3d_toy_prog",
+    "v_3d_toy_prog_execute",
     "v_3d_toy_prog_params",
 ]