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

niwrap_afni/afni/v_3d_tproject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TPROJECT_METADATA = Metadata(
-    id="f0bb8b9be73d7fb85ec362ec946cfdb828647c25.boutiques",
+    id="25cd37518a6caddf1b9adfcbce854a948d625c5f.boutiques",
     name="3dTproject",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,27 @@ V_3D_TPROJECT_METADATA = Metadata(
 
 
 V3dTprojectParameters = typing.TypedDict('V3dTprojectParameters', {
-    "__STYXTYPE__": typing.Literal["3dTproject"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTproject"]],
+    "TR": typing.NotRequired[float | None],
+    "automask": bool,
+    "bandpass": typing.NotRequired[list[float] | None],
+    "blur": typing.NotRequired[float | None],
+    "cenmode": typing.NotRequired[typing.Literal["kill", "zero", "ntrp"] | None],
+    "censor": typing.NotRequired[InputPathType | None],
+    "censortr": typing.NotRequired[list[str] | None],
+    "concat": typing.NotRequired[InputPathType | None],
+    "dsort": typing.NotRequired[list[InputPathType] | None],
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "noblock": bool,
+    "norm": bool,
+    "ort": typing.NotRequired[InputPathType | None],
+    "polort": typing.NotRequired[int | None],
+    "stopband": typing.NotRequired[list[float] | None],
+    "prefix": str,
+})
+V3dTprojectParametersTagged = typing.TypedDict('V3dTprojectParametersTagged', {
+    "@type": typing.Literal["afni/3dTproject"],
     "TR": typing.NotRequired[float | None],
     "automask": bool,
     "bandpass": typing.NotRequired[list[float] | None],
@@ -33,43 +53,11 @@ V3dTprojectParameters = typing.TypedDict('V3dTprojectParameters', {
     "stopband": typing.NotRequired[list[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 {
-        "3dTproject": v_3d_tproject_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 {
-        "3dTproject": v_3d_tproject_outputs,
-    }.get(t)
 
 
 class V3dTprojectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tproject(...)`.
+    Output object returned when calling `V3dTprojectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +83,7 @@ def v_3d_tproject_params(
     ort: InputPathType | None = None,
     polort: int | None = None,
     stopband: list[float] | None = None,
-) -> V3dTprojectParameters:
+) -> V3dTprojectParametersTagged:
     """
     Build parameters.
     
@@ -168,7 +156,7 @@ def v_3d_tproject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTproject",
+        "@type": "afni/3dTproject",
         "automask": automask,
         "in_file": in_file,
         "noblock": noblock,
@@ -217,79 +205,79 @@ def v_3d_tproject_cargs(
     """
     cargs = []
     cargs.append("3dTproject")
-    if params.get("TR") is not None:
+    if params.get("TR", None) is not None:
         cargs.extend([
             "-TR",
-            str(params.get("TR"))
+            str(params.get("TR", None))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("bandpass") is not None:
+    if params.get("bandpass", None) is not None:
         cargs.extend([
             "-bandpass",
-            *map(str, params.get("bandpass"))
+            *map(str, params.get("bandpass", None))
         ])
-    if params.get("blur") is not None:
+    if params.get("blur", None) is not None:
         cargs.extend([
             "-blur",
-            str(params.get("blur"))
+            str(params.get("blur", None))
         ])
-    if params.get("cenmode") is not None:
+    if params.get("cenmode", None) is not None:
         cargs.extend([
             "-cenmode",
-            params.get("cenmode")
+            params.get("cenmode", None)
         ])
-    if params.get("censor") is not None:
+    if params.get("censor", None) is not None:
         cargs.extend([
             "-censor",
-            execution.input_file(params.get("censor"))
+            execution.input_file(params.get("censor", None))
         ])
-    if params.get("censortr") is not None:
+    if params.get("censortr", None) is not None:
         cargs.extend([
             "-CENSORTR",
-            *params.get("censortr")
+            *params.get("censortr", None)
         ])
-    if params.get("concat") is not None:
+    if params.get("concat", None) is not None:
         cargs.extend([
             "-concat",
-            execution.input_file(params.get("concat"))
+            execution.input_file(params.get("concat", None))
         ])
-    if params.get("dsort") is not None:
+    if params.get("dsort", None) is not None:
         cargs.extend([
             "-dsort",
-            *[execution.input_file(f) for f in params.get("dsort")]
+            *[execution.input_file(f) for f in params.get("dsort", None)]
         ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("in_file"))
+        execution.input_file(params.get("in_file", None))
     ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("noblock"):
+    if params.get("noblock", False):
         cargs.append("-noblock")
-    if params.get("norm"):
+    if params.get("norm", False):
         cargs.append("-norm")
-    if params.get("ort") is not None:
+    if params.get("ort", None) is not None:
         cargs.extend([
             "-ort",
-            execution.input_file(params.get("ort"))
+            execution.input_file(params.get("ort", None))
         ])
-    if params.get("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polort"))
+            str(params.get("polort", None))
         ])
-    if params.get("stopband") is not None:
+    if params.get("stopband", None) is not None:
         cargs.extend([
             "-stopband",
-            *map(str, params.get("stopband"))
+            *map(str, params.get("stopband", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     return cargs
 
@@ -309,21 +297,24 @@ def v_3d_tproject_outputs(
     """
     ret = V3dTprojectOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")),
+        out_file=execution.output_file(params.get("prefix", None)),
     )
     return ret
 
 
 def v_3d_tproject_execute(
     params: V3dTprojectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTprojectOutputs:
     """
-    This program projects (detrends) out various 'nuisance' time series from each
-    voxel in the input dataset. Note that all the projections are done via linear
-    regression, including the frequency-based options such as '-passband'. In this
-    way, you can bandpass time-censored data, and at the same time, remove other
-    time series of no interest (e.g., physiological estimates, motion parameters).
+    3dTproject
+    
+    This program projects (detrends) out various 'nuisance' time series from
+    each voxel in the input dataset. Note that all the projections are done via
+    linear regression, including the frequency-based options such as
+    '-passband'. In this way, you can bandpass time-censored data, and at the
+    same time, remove other time series of no interest (e.g., physiological
+    estimates, motion parameters).
     
     Author: AFNI Developers
     
@@ -331,10 +322,12 @@ def v_3d_tproject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTprojectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TPROJECT_METADATA)
     params = execution.params(params)
     cargs = v_3d_tproject_cargs(params, execution)
     ret = v_3d_tproject_outputs(params, execution)
@@ -363,11 +356,14 @@ def v_3d_tproject(
     runner: Runner | None = None,
 ) -> V3dTprojectOutputs:
     """
-    This program projects (detrends) out various 'nuisance' time series from each
-    voxel in the input dataset. Note that all the projections are done via linear
-    regression, including the frequency-based options such as '-passband'. In this
-    way, you can bandpass time-censored data, and at the same time, remove other
-    time series of no interest (e.g., physiological estimates, motion parameters).
+    3dTproject
+    
+    This program projects (detrends) out various 'nuisance' time series from
+    each voxel in the input dataset. Note that all the projections are done via
+    linear regression, including the frequency-based options such as
+    '-passband'. In this way, you can bandpass time-censored data, and at the
+    same time, remove other time series of no interest (e.g., physiological
+    estimates, motion parameters).
     
     Author: AFNI Developers
     
@@ -442,8 +438,6 @@ def v_3d_tproject(
     Returns:
         NamedTuple of outputs (described in `V3dTprojectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TPROJECT_METADATA)
     params = v_3d_tproject_params(
         tr=tr,
         automask=automask,
@@ -463,13 +457,13 @@ def v_3d_tproject(
         stopband=stopband,
         prefix=prefix,
     )
-    return v_3d_tproject_execute(params, execution)
+    return v_3d_tproject_execute(params, runner)
 
 
 __all__ = [
     "V3dTprojectOutputs",
-    "V3dTprojectParameters",
     "V_3D_TPROJECT_METADATA",
     "v_3d_tproject",
+    "v_3d_tproject_execute",
     "v_3d_tproject_params",
 ]

niwrap_afni/afni/v_3d_tqual.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TQUAL_METADATA = Metadata(
-    id="b10cb749ab7883032d18c3d65d9aa72239852046.boutiques",
+    id="0de10e9fb49d56a5dd962153bd916ab621b35ca3.boutiques",
     name="3dTqual",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_TQUAL_METADATA = Metadata(
 
 
 V3dTqualParameters = typing.TypedDict('V3dTqualParameters', {
-    "__STYXTYPE__": typing.Literal["3dTqual"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTqual"]],
+    "dataset": InputPathType,
+    "spearman": bool,
+    "quadrant": bool,
+    "autoclip": bool,
+    "automask": bool,
+    "clip": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "range": bool,
+})
+V3dTqualParametersTagged = typing.TypedDict('V3dTqualParametersTagged', {
+    "@type": typing.Literal["afni/3dTqual"],
     "dataset": InputPathType,
     "spearman": bool,
     "quadrant": bool,
@@ -24,43 +35,11 @@ V3dTqualParameters = typing.TypedDict('V3dTqualParameters', {
     "mask": typing.NotRequired[InputPathType | None],
     "range": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTqual": v_3d_tqual_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 {
-        "3dTqual": v_3d_tqual_outputs,
-    }.get(t)
 
 
 class V3dTqualOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tqual(...)`.
+    Output object returned when calling `V3dTqualParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_tqual_params(
     clip: float | None = None,
     mask: InputPathType | None = None,
     range_: bool = False,
-) -> V3dTqualParameters:
+) -> V3dTqualParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +80,7 @@ def v_3d_tqual_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTqual",
+        "@type": "afni/3dTqual",
         "dataset": dataset,
         "spearman": spearman,
         "quadrant": quadrant,
@@ -131,26 +110,26 @@ def v_3d_tqual_cargs(
     """
     cargs = []
     cargs.append("3dTqual")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("spearman"):
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("spearman", False):
         cargs.append("-spearman")
-    if params.get("quadrant"):
+    if params.get("quadrant", False):
         cargs.append("-quadrant")
-    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("clip") is not None:
+    if params.get("clip", None) is not None:
         cargs.extend([
             "-clip",
-            str(params.get("clip"))
+            str(params.get("clip", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("range"):
+    if params.get("range", False):
         cargs.append("-range")
     return cargs
 
@@ -177,9 +156,11 @@ def v_3d_tqual_outputs(
 
 def v_3d_tqual_execute(
     params: V3dTqualParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTqualOutputs:
     """
+    3dTqual
+    
     Computes a quality index for each sub-brick in a 3D+time dataset.
     
     Author: AFNI Developers
@@ -188,10 +169,12 @@ def v_3d_tqual_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTqualOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TQUAL_METADATA)
     params = execution.params(params)
     cargs = v_3d_tqual_cargs(params, execution)
     ret = v_3d_tqual_outputs(params, execution)
@@ -211,6 +194,8 @@ def v_3d_tqual(
     runner: Runner | None = None,
 ) -> V3dTqualOutputs:
     """
+    3dTqual
+    
     Computes a quality index for each sub-brick in a 3D+time dataset.
     
     Author: AFNI Developers
@@ -237,8 +222,6 @@ def v_3d_tqual(
     Returns:
         NamedTuple of outputs (described in `V3dTqualOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TQUAL_METADATA)
     params = v_3d_tqual_params(
         dataset=dataset,
         spearman=spearman,
@@ -249,13 +232,13 @@ def v_3d_tqual(
         mask=mask,
         range_=range_,
     )
-    return v_3d_tqual_execute(params, execution)
+    return v_3d_tqual_execute(params, runner)
 
 
 __all__ = [
     "V3dTqualOutputs",
-    "V3dTqualParameters",
     "V_3D_TQUAL_METADATA",
     "v_3d_tqual",
+    "v_3d_tqual_execute",
     "v_3d_tqual_params",
 ]